Mercurial > repos > iuc > samtools_view
annotate samtools_view.xml @ 17:32dc5f781059 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
author | iuc |
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date | Sun, 08 Sep 2024 03:27:39 +0000 |
parents | 2dce91e11ca7 |
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rev | line source |
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2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
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changeset
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1 <tool id="samtools_view" name="Samtools view" version="@TOOL_VERSION@+galaxy3" profile="@PROFILE@"> |
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b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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2 <description>- reformat, filter, or subsample SAM, BAM or CRAM</description> |
0
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
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3 <macros> |
7
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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4 <import>macros.xml</import> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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5 <token name="@REF_DATA@"> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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6 ## additional reference data |
12
c370440f901e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit c5ded4208dd70e88596ddc725795a2401773f02d"
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7 #if $use_ref: |
c370440f901e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit c5ded4208dd70e88596ddc725795a2401773f02d"
iuc
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8 -T "\$reffa" |
c370440f901e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit c5ded4208dd70e88596ddc725795a2401773f02d"
iuc
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9 -t "\$reffai" |
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b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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10 #end if |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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11 </token> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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12 <xml name="read_output_formatting"> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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13 <yield /> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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14 <section name="adv_output" title="Read Reformatting Options" expanded="false"> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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15 <repeat name="readtags" title="Strip read tags from output"> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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16 <param name="readtag" type="text" argument="-x" label="Read tag to strip" help="Read tag to exclude from output."/> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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17 </repeat> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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18 <param name="collapsecigar" type="boolean" argument="-B" truevalue="-B" falsevalue="" checked="false" label="Collapse backward CIGAR operation" help="Collapse the backward CIGAR operation." /> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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19 </section> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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20 </xml> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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21 <xml name="output_format_selector"> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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22 <conditional name="output_format"> |
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bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
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23 <param name="oformat" type="select" label="Output format" |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
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24 help="Note on BAM output format: The tool will generate coordinate-sorted BAM, i.e., may change the order of reads compared to the input. For BAM input, select 'Same as input' to produce BAM output with the read order retained."> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
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25 <option value="input">Same as input</option> |
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b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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26 <option value="sam">SAM</option> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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27 <option value="bam" selected="True">BAM (-b)</option> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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28 <option value="cram">CRAM (-C)</option> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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29 </param> |
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bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
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30 <when value="input" /> |
7
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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31 <when value="sam"> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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32 <yield /> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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33 </when> |
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bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
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34 <when value="bam" /> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
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35 <when value="cram" /> |
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b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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36 </conditional> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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37 </xml> |
0
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
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38 </macros> |
2
02afb5ea2fce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
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39 <expand macro="requirements"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1354b1358df89a922c3243f7e27ce789094b8644"
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40 <requirement type="package" version="5.1.0">gawk</requirement> |
2
02afb5ea2fce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
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41 </expand> |
0
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
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42 <expand macro="stdio"/> |
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
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43 <expand macro="version_command"/> |
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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44 <command><![CDATA[ |
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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45 @ADDTHREADS@ |
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b72793637686
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit d15d26f8596e3220fa7aadc76e8623d42b27280d"
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46 @ADDMEMORY@ |
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00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
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47 ## prepare reference data |
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
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48 @PREPARE_FASTA_IDX@ |
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
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49 @PREPARE_IDX@ |
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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50 |
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bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
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51 ## determine the output format flag to pass to samtools view |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
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52 ## -c for count mode |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
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53 ## -b to produce BAM-formatted output |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
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54 ## -C to produce CRAM-formatted output |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
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55 ## SAM is the default ouput format |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
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56 #set $fmtopt = '' |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
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57 #if str($mode.output_options.reads_report_type) == 'count': |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
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58 #set $fmtopt = '-c' |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
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59 #else: |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
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60 #if str($mode.output_options.output_format.oformat) == 'bam': |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
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61 #set $fmtopt = '-b' |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
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62 #elif str($mode.output_options.output_format.oformat) == 'cram': |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
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63 #set $fmtopt = '-C' |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
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64 #elif str($mode.output_options.output_format.oformat) == 'input': |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
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65 #if $input.is_of_type('bam'): |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
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66 #set $fmtopt = '-b' |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
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67 #elif $input.is_of_type('cram'): |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
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68 #set $fmtopt = '-C' |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
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69 #else: |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
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70 ## input in SAM format, make sure to keep header if present |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
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71 #set $fmtopt = '-h' |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
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72 #end if |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
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73 #end if |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
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74 #end if |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
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|
75 |
7
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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|
76 #if str($mode.outtype) == 'header': |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
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|
77 ## call samtools view and be done |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
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|
78 samtools view |
8
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
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79 -H $fmtopt -o outfile |
7
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
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80 @REF_DATA@ |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
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|
81 infile |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
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|
82 #else: |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
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|
83 ## are filtering and/or subsampling in effect? |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
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|
84 #set $with_filtering = False |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
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|
85 #set $with_subsampling = False |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
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changeset
|
86 #if str($mode.outtype) == 'selected_reads': |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
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87 #set $with_filtering = True |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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88 #if str($mode.subsample_config.subsampling_mode.select_subsample) != 'fraction' or $mode.subsample_config.subsampling_mode.factor > 1: |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
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89 #set $with_subsampling = True |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
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90 #end if |
0
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
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91 #end if |
7
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
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|
92 |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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93 ## are we producing one or two outputs? |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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94 #if str($mode.outtype) == 'selected_reads' and str($mode.output_options.reads_report_type) != 'count' and str($mode.output_options.complementary_output) == 'yes': |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
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95 #set $with_non_selected_reads_output = True |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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96 #else: |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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97 #set $with_non_selected_reads_output = False |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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98 #end if |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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99 |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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100 #set $std_filters = '' |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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101 #set $reg_filters = '' |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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102 #if $with_filtering: |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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103 ## build string of all user-configured filter options |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
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104 #if str($mode.filter_config.cond_region.select_region) == 'bed': |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
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105 #set std_filters = $std_filters + " -L '%s'" % str($mode.filter_config.cond_region.bedfile) |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
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106 #elif str($mode.filter_config.cond_region.select_region) == 'text': |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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107 #set $reg_filters = "'%s'" % str($mode.filter_config.cond_region.regions).strip() |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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108 #end if |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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109 |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
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110 #if $mode.filter_config.cond_rg.select_rg == 'text': |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
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111 #set $std_filters = $std_filters + " -r '%s'" % str($mode.filter_config.cond_rg.readgr) |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
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112 #else if $mode.filter_config.cond_rg.select_rg == 'file': |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
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113 #set $std_filters = $std_filters + " -R '%s'" % str($mode.filter_config.cond_rg.rgfile) |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
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114 #end if |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
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|
115 #if str($mode.filter_config.quality) != '' and int($mode.filter_config.quality) > 0: |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
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116 #set $std_filters = $std_filters + " -q %s" % str($mode.filter_config.quality) |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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117 #end if |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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118 #if str($mode.filter_config.library): |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
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119 #set $std_filters = $std_filters + " -l '%s'" % str($mode.filter_config.library) |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
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120 #end if |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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121 #if str($mode.filter_config.cigarcons): |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
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122 #set $std_filters = $std_filters + " -m %s" % str($mode.filter_config.cigarcons) |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
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|
123 #end if |
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
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124 #set $filter = $mode.filter_config.inclusive_filter |
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
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125 @FLAGS@ |
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
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126 #set $std_filters = $std_filters + " -f %s" % str($flags) |
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
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127 #set $filter = $mode.filter_config.exclusive_filter |
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
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|
128 @FLAGS@ |
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
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129 #set $std_filters = $std_filters + " -F %s" % str($flags) |
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
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130 #set $filter = $mode.filter_config.exclusive_filter_all |
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
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|
131 @FLAGS@ |
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
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132 #set $std_filters = $std_filters + " -G %s" % str($flags) |
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
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133 #if $mode.filter_config.tag: |
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
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134 #set $std_filters = $std_filters + " --tag '%s'" % $mode.filter_config.tag |
7
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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|
135 #end if |
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
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|
136 #if $mode.filter_config.qname_file: |
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
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|
137 #set std_filters = $std_filters + " --qname-file '%s'" % $mode.filter_config.qname_file |
2
02afb5ea2fce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
iuc
parents:
1
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|
138 #end if |
16
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
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|
139 #if str($cond_expr.select_expr) == "yes": |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
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140 #set std_filters = $std_filters + " -e '%s'" % $cond_expr.expression |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
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|
141 #end if |
0
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
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|
142 #end if |
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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|
143 |
7
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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|
144 #if $with_subsampling: |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
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|
145 ## handle seed and fraction calculation for subsampling |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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146 #import random |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
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|
147 #if str($mode.subsample_config.subsampling_mode.seed): |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
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148 #set $seed = int($mode.subsample_config.subsampling_mode.seed) |
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149 #else: |
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150 #set $seed = random.randrange(32768) |
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151 #end if |
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152 |
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153 #if $mode.subsample_config.subsampling_mode.select_subsample == 'target': |
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154 ##this must be done before the main command because we don't know the total # reads until execution time |
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155 #if $input.is_of_type('sam') or $std_filters or $reg_filters: |
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156 ## There is no index or we cannot use it because we are |
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157 ## not dealing with all of the reads in the indexed |
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158 ## file. We have to do an extra pass over the input to |
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159 ## count the reads to subsample. |
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160 sample_fragment=`samtools view -c $std_filters infile $reg_filters | awk '{s=\$1} END {fac=s/${mode.subsample_config.subsampling_mode.target}; printf("%.8f\n", fac > 1 ? 1/fac : 1)}'` && |
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161 #else: |
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162 ## We can get the count of reads to subsample using |
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163 ## an inexpensive call to idxstats. |
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164 sample_fragment=`samtools idxstats infile | awk '{s+=\$4+\$3} END {fac=s/${mode.subsample_config.subsampling_mode.target}; printf("%.8f\n", fac > 1 ? 1/fac : 1)}'` && |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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165 #end if |
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166 #end if |
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167 #end if |
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168 |
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169 ## call samtools view |
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170 samtools view |
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171 -@ \$addthreads |
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172 $fmtopt |
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173 |
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174 ## filter options (except regions filter, which is the last parameter) |
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175 $std_filters |
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176 #if $with_subsampling: |
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177 --subsample-seed $seed |
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178 #if str($mode.subsample_config.subsampling_mode.select_subsample) == "target": |
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179 ##this is calculated at execution time before the main samtools command |
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180 --subsample \${sample_fragment} |
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181 #else: |
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182 #set $fraction = 1 / float($mode.subsample_config.subsampling_mode.factor) |
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183 --subsample $fraction |
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184 #end if |
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185 #end if |
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186 |
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187 ## output options |
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188 #if str($mode.output_options.reads_report_type) == 'count': |
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189 -o outfile |
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190 #else: |
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191 ## output options |
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192 #if str($mode.output_options.output_format.oformat) == 'sam': |
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193 ${mode.output_options.output_format.with_header} |
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194 #end if |
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195 ${mode.output_options.adv_output.collapsecigar} |
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196 #for $s in $mode.output_options.adv_output.readtags: |
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197 -x '${s.readtag}' |
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198 #end for |
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199 #if str($mode.output_options.reads_report_type) == 'retained' |
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200 -o outfile |
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201 #if $with_non_selected_reads_output: |
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202 -U inv_outfile |
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203 #end if |
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204 #else: |
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205 -U outfile |
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206 #if $with_non_selected_reads_output: |
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207 -o inv_outfile |
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208 #else: |
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209 -o /dev/null |
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210 #end if |
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211 #end if |
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212 |
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213 ##currently reference based CRAM is disabled (see https://github.com/galaxyproject/tools-iuc/pull/1963) |
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214 #if $mode.output_options.output_format.oformat == 'cram': |
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215 --output-fmt-option no_ref |
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216 #end if |
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217 #end if |
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218 |
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219 @REF_DATA@ |
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220 |
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221 infile |
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222 |
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223 ## region filter needs to be at the end |
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224 $reg_filters |
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225 |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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226 #if str($mode.output_options.reads_report_type) != 'count': |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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227 ## if data is converted from an unsorted file (SAM, CRAM, or unsorted BAM) to BAM |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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228 ## then sort the output by coordinate, |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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229 #if not $input.is_of_type('bam') and str($mode.output_options.output_format.oformat) == 'bam': |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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230 && samtools sort |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit d15d26f8596e3220fa7aadc76e8623d42b27280d"
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231 -@ \$addthreads -m \$addmemory"M" -T "\${TMPDIR:-.}" |
7
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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232 -O bam |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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233 -o tmpsam |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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234 outfile |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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235 && mv tmpsam outfile |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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236 #if $with_non_selected_reads_output: |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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237 && samtools sort |
9
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit d15d26f8596e3220fa7aadc76e8623d42b27280d"
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238 -@ \$addthreads -m \$addmemory"M" -T "\${TMPDIR:-.}" |
7
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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239 -O bam |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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240 -o tmpsam |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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241 inv_outfile |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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242 && mv tmpsam inv_outfile |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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243 #end if |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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244 #end if |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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245 #end if |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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246 |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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247 ##end of reads and count-specific section |
0
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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248 #end if |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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249 ]]></command> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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250 <inputs> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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251 <!-- note unsorted bam includes all derived bam types (inlcuding bam which is sorted) --> |
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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252 <param name="input" format="sam,unsorted.bam,cram" type="data" label="SAM/BAM/CRAM data set" /> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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253 <conditional name="mode"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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254 <param name="outtype" type="select" label="What would you like to look at?"> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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255 <option value="all_reads">All reads in the input dataset</option> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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256 <option value="selected_reads">A filtered/subsampled selection of reads</option> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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257 <option value="header">Just the input header (-H)</option> |
0
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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258 </param> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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259 <when value="all_reads"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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260 <conditional name="output_options"> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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261 <param name="reads_report_type" type="select" label="What would you like to have reported?"> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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262 <option value="retained">The actual reads</option> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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263 <option value="count">The count of reads (-c)</option> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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264 </param> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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265 <when value="retained"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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266 <expand macro="read_output_formatting" /> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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267 <expand macro="output_format_selector"> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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268 <param name="with_header" type="boolean" truevalue="-h" falsevalue="" checked="True" |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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269 label="Include SAM header in the output?" /> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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270 </expand> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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271 </when> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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272 <when value="count" /> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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273 </conditional> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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274 </when> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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275 <when value="selected_reads"> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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276 <section name="filter_config" title="Configure filters" expanded="false"> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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277 <conditional name="cond_region"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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278 <param name="select_region" type="select" label="Filter by regions"> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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279 <option value="no" selected="True">No</option> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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280 <option value="text">Manualy specify regions</option> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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281 <option value="bed">Regions from BED file</option> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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282 </param> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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283 <when value="no"/> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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284 <when value="text"> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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285 <param name="regions" type="text" optional="false" label="Filter by regions" help="One or more space-separated region specifications to restrict output to only those alignments which overlap the specified region(s)."/> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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286 </when> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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287 <when value="bed"> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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288 <param name="bedfile" format="bed" argument="-L" optional="false" type="data" label="Filter by intervals in a bed file" help="Only output alignments overlapping the intervals in the input bed file." /> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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289 </when> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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290 </conditional> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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291 <conditional name="cond_rg"> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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292 <param name="select_rg" type="select" label="Filter by readgroup"> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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293 <option value="no" selected="True">No</option> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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294 <option value="text">Single read group </option> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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295 <option value="file">Read groups from file</option> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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296 </param> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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297 <when value="no"/> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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298 <when value="text"> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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299 <param name="readgr" type="text" argument="-r" label="Filter by read group" help="Only output alignments in read group." /> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
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|
300 </when> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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301 <when value="file"> |
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302 <param name="rgfile" type="data" format="tabular" argument="-R" label="Filter by read groups in file" help="Output alignments in read groups listed in FILE." /> |
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303 </when> |
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304 </conditional> |
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305 <conditional name="cond_expr"> |
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306 <param name="select_expr" type="select" label="Filter by expression"> |
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307 <option value="no" selected="True">No</option> |
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308 <option value="yes">Filter using an expression (see manual)</option> |
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309 </param> |
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310 <when value="no"/> |
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311 <when value="yes"> |
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312 <param name="expression" type="text" argument="-e" label="Filter by expression - for example sclen>0 will filter all soft clipped reads" help="See Samtools manual for Filter expression syntax"> |
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313 <sanitizer invalid_char=""> |
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314 <valid initial="string.printable"> |
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315 <remove value="'"/> |
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316 </valid> |
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317 </sanitizer> |
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318 </param> |
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319 </when> |
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320 </conditional> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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321 <param name="quality" type="integer" argument="-q" optional="true" min="0" label="Filter by quality" help="Skip alignments with MAPQ smaller than INT." /> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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322 <param name="library" type="text" argument="-l" optional="true" label="Filter by library" help="Only output alignments in library STR" /> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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323 <param name="cigarcons" type="integer" argument="-m" optional="true" min="0" label="Filter by number of CIGAR bases consuming query sequence" help="Only output alignments with number of CIGAR bases consuming query sequence greater than or equal INT." /> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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324 <param name="inclusive_filter" argument="-f" type="select" multiple="True" label="Require that these flags are set"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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325 <expand macro="flag_options" /> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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326 </param> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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327 <param name="exclusive_filter" argument="-F" type="select" multiple="True" label="Exclude reads with any of the following flags set"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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328 <expand macro="flag_options" /> |
0
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329 </param> |
7
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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330 <param name="exclusive_filter_all" argument="-G" type="select" multiple="True" label="Exclude reads with all of the following flags set"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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331 <expand macro="flag_options" /> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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332 </param> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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333 <param argument="--tag" type="text" optional="true" label="Filter by tag" help="Only include reads with tag STR1 and associated value STR2. Write in the format STR1:STR2 (see help for more details)." /> |
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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334 <!-- TODO implement -D --> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1d2666cfe206ef538fd811dbccaec2e8f3c6f7f0"
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335 <param argument="--qname-file" format="txt" optional="true" type="data" label="Filter by readnames" help="Only output alignments with readnames that are listed in this file." /> |
7
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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336 </section> |
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337 <section name="subsample_config" title="Configure subsampling" expanded="false"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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338 <conditional name="subsampling_mode"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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339 <param name="select_subsample" type="select" argument="-s" label="Subsample alignment"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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340 <option value="fraction">Specify a downsampling factor</option> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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341 <option value="target">Specify a target # of reads</option> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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342 </param> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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343 <when value="fraction"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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344 <param name="factor" type="float" optional="False" value="1" min="1" label="Downsampling factor" help="The factor by which to downsample the input reads. A fraction of approx. 1/factor of the reads will be kept (default: 1 = no downsampling)." /> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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345 <expand macro="seed_input" /> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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346 </when> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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347 <when value="target"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
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348 <param name="target" type="integer" optional="False" min="1" value="" label="Target # of reads" help="Sets the approx. target number of reads to subsample." /> |
7
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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349 <expand macro="seed_input" /> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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350 </when> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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351 </conditional> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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352 </section> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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353 <conditional name="output_options"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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354 <param name="reads_report_type" type="select" |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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355 label="What would you like to have reported?" |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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356 help="Hint: To invert all of the filtering/subsampling logic configured above, choose 'Reads dropped during filtering and subsampling'."> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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357 <option value="retained">All reads retained after filtering and subsampling</option> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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358 <option value="dropped">Reads dropped during filtering and subsampling</option> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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359 <option value="count">The count of retained reads (-c)</option> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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360 </param> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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361 <when value="retained"> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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362 <expand macro="read_output_formatting"> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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363 <param name="complementary_output" type="boolean" truevalue="yes" falsevalue="no" checked="false" |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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364 label="Produce extra dataset with dropped reads?" /> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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365 </expand> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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366 <expand macro="output_format_selector"> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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367 <param name="with_header" type="boolean" truevalue="-h" falsevalue="" checked="True" |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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368 label="Include SAM header in the output?" /> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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369 </expand> |
0
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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370 </when> |
7
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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371 <when value="dropped"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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372 <expand macro="read_output_formatting"> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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373 <param name="complementary_output" type="boolean" truevalue="yes" falsevalue="no" checked="false" |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
374 label="Produce extra dataset with retained reads?" /> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
375 </expand> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
376 <expand macro="output_format_selector"> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
377 <param name="with_header" type="boolean" truevalue="-h" falsevalue="" checked="True" |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
378 label="Include SAM header in the output?" /> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
379 </expand> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
380 </when> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
381 <when value="count" /> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
382 </conditional> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
383 </when> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
384 <when value="header"> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
385 <conditional name="output_options"> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
386 <param name="reads_report_type" type="select" label="What would you like to have reported?"> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
387 <option value="">The header in ...</option> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
388 </param> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
389 <when value=""> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
390 <expand macro="output_format_selector" /> |
0
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
391 </when> |
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
392 </conditional> |
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
393 </when> |
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
394 </conditional> |
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
395 <expand macro="optional_reference" argument="-t" help="Reference data as fasta(.gz). Required for SAM input without @SQ headers and useful/required for writing CRAM output (see help)."/> |
0
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
396 </inputs> |
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
397 <outputs> |
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
398 <!-- TODO do I need an action for dbkey? --> |
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
399 <data name="outputsam" format_source="input" from_work_dir="outfile" label="${tool.name} on ${on_string}: filtered alignments"> |
7
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
400 <filter>mode['outtype'] == 'header' or mode['output_options']['reads_report_type'] != 'count'</filter> |
0
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
401 <change_format> |
7
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
402 <when input="mode.output_options.output_format.oformat" value="sam" format="sam" /> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
403 <when input="mode.output_options.output_format.oformat" value="bam" format="bam" /> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
404 <when input="mode.output_options.output_format.oformat" value="cram" format="cram" /> |
0
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
405 </change_format> |
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
406 </data> |
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
407 <data name="invoutputsam" format_source="input" from_work_dir="inv_outfile" label="${tool.name} on ${on_string}: unfiltered alignments"> |
7
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
408 <filter>mode['outtype'] == 'selected_reads' and mode['output_options']['reads_report_type'] != 'count' and mode['output_options']['complementary_output']</filter> |
0
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
409 <change_format> |
7
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
410 <when input="mode.output_options.output_format.oformat" value="sam" format="sam" /> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
411 <when input="mode.output_options.output_format.oformat" value="bam" format="bam" /> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
412 <when input="mode.output_options.output_format.oformat" value="cram" format="cram" /> |
0
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
413 </change_format> |
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
414 </data> |
8
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
415 <data name="outputcnt" format="tabular" from_work_dir="outfile" label="${tool.name} on ${on_string}: Counts"> |
7
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
416 <filter>mode['outtype'] != 'header' and mode['output_options']['reads_report_type'] == 'count'</filter> |
0
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
417 </data> |
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
418 </outputs> |
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
419 <tests> |
15
6be888be75f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents:
14
diff
changeset
|
420 <!-- 1) sam to bam (copied from the sam_to_bam tool) --> |
6be888be75f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents:
14
diff
changeset
|
421 <test expect_num_outputs="1"> |
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
422 <param name="input" ftype="sam" value="in_test_1.sam" /> |
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
423 <output name="outputsam" ftype="bam" file="test_1.bam" lines_diff="4" /> |
0
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
424 </test> |
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
425 <!-- 2) --> |
15
6be888be75f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents:
14
diff
changeset
|
426 <test expect_num_outputs="1"> |
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
427 <param name="input" ftype="sam" dbkey="equCab2" value="in_test_1.sam" /> |
0
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
428 <conditional name="addref_cond"> |
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
429 <param name="addref_select" value="cached" /> |
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
430 <param name="ref" value="equCab2chrM" /> |
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
431 </conditional> |
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
432 <output name="outputsam" ftype="bam" file="test_2.bam" lines_diff="4" /> |
0
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
433 </test> |
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
434 <!-- 3) --> |
15
6be888be75f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents:
14
diff
changeset
|
435 <test expect_num_outputs="1"> |
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
436 <param name="input" ftype="sam" value="in_test_3.sam" /> |
0
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
437 <conditional name="addref_cond"> |
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
438 <param name="addref_select" value="history" /> |
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
439 <param name="ref" ftype="fasta" dbkey="equCab2" value="chr_m.fasta" /> |
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
440 </conditional> |
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
441 <output name="outputsam" ftype="bam" file="test_3.bam" lines_diff="4" /> |
0
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
442 </test> |
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
443 <!-- 4) cram to bam --> |
15
6be888be75f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents:
14
diff
changeset
|
444 <test expect_num_outputs="1"> |
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
445 <param name="input" value="in_test_4.cram" ftype="cram" /> |
0
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
446 <conditional name="addref_cond"> |
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
447 <param name="addref_select" value="history" /> |
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
448 <param name="ref" value="test.fa" /> |
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
449 </conditional> |
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
450 <output name="outputsam" file="test_4.bam" ftype="bam" lines_diff="4" /> |
0
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
451 </test> |
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
452 <!-- 5) within bam operations expected to result in sorting or not --> |
15
6be888be75f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents:
14
diff
changeset
|
453 <test expect_num_outputs="1"> |
8
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
454 <!-- sorted bam should always result in unmodifed output --> |
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
455 <param name="input" ftype="bam" value="in_test_5.bam" /> |
8
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
456 <assert_command> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
457 <not_has_text text="samtools sort" /> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
458 </assert_command> |
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
459 <output name="outputsam" ftype="bam" file="test_5.bam" lines_diff="2"/> |
4
fdc58a0cc1d4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 640b53919bfc0ae4b895451218e919a52ac14b9d
iuc
parents:
2
diff
changeset
|
460 </test> |
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
461 <!-- 6) --> |
15
6be888be75f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents:
14
diff
changeset
|
462 <test expect_num_outputs="1"> |
8
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
463 <!-- sorted bam should always result in unmodifed output --> |
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
464 <param name="input" ftype="bam" value="in_test_5.bam" /> |
7
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
465 <conditional name="mode"> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
466 <conditional name="output_options"> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
467 <conditional name="output_format"> |
8
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
468 <param name="oformat" value="input" /> |
7
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
469 </conditional> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
470 </conditional> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
471 </conditional> |
8
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
472 <assert_command> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
473 <not_has_text text="samtools sort" /> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
474 </assert_command> |
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
475 <output name="outputsam" ftype="bam" file="test_5.bam" lines_diff="2"/> |
0
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
476 </test> |
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
477 <!-- 7) --> |
15
6be888be75f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents:
14
diff
changeset
|
478 <test expect_num_outputs="1"> |
8
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
479 <!-- qname_sorted.bam should get sorted during "conversion" to bam ... --> |
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
480 <param name="input" ftype="qname_sorted.bam" value="in_test_7.bam" /> |
8
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
481 <assert_command> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
482 <has_text text="samtools sort" /> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
483 </assert_command> |
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
484 <output name="outputsam" ftype="bam" file="test_7.bam" lines_diff="4" /> |
8
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
485 </test> |
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
486 <!-- 8) --> |
15
6be888be75f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents:
14
diff
changeset
|
487 <test expect_num_outputs="1"> |
8
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
488 <!-- ... but should be emitted unmodifed when using input format --> |
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
489 <param name="input" ftype="qname_sorted.bam" value="in_test_7.bam" /> |
7
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
490 <conditional name="mode"> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
491 <conditional name="output_options"> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
492 <conditional name="output_format"> |
8
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
493 <param name="oformat" value="input" /> |
7
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
494 </conditional> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
495 </conditional> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
496 </conditional> |
8
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
497 <assert_command> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
498 <not_has_text text="samtools sort" /> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
499 </assert_command> |
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
500 <output name="outputsam" ftype="qname_sorted.bam" file="test_8.bam" lines_diff="2"/> |
8
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
501 </test> |
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
502 <!-- 9) --> |
15
6be888be75f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents:
14
diff
changeset
|
503 <test expect_num_outputs="1"> |
8
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
504 <!-- unsorted.bam should get sorted during "conversion" to bam ... --> |
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
505 <param name="input" ftype="unsorted.bam" value="in_test_7.bam" /> |
8
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
506 <assert_command> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
507 <has_text text="samtools sort" /> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
508 </assert_command> |
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
509 <output name="outputsam" ftype="bam" file="test_7.bam" lines_diff="4" /> |
8
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
510 </test> |
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
511 <!-- 10) --> |
15
6be888be75f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents:
14
diff
changeset
|
512 <test expect_num_outputs="1"> |
8
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
513 <!-- ... ... but should be emitted unmodifed when using input format --> |
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
514 <param name="input" ftype="unsorted.bam" value="in_test_7.bam" /> |
8
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
515 <conditional name="mode"> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
516 <conditional name="output_options"> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
517 <conditional name="output_format"> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
518 <param name="oformat" value="input" /> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
519 </conditional> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
520 </conditional> |
0
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
521 </conditional> |
8
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
522 <assert_command> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
523 <not_has_text text="samtools sort" /> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
524 </assert_command> |
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
525 <output name="outputsam" ftype="unsorted.bam" file="test_8.bam" lines_diff="2" /> |
0
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
526 </test> |
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
527 <!-- 11) bam to sam + header options (adapted from bam_to_sam tool)--> |
15
6be888be75f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents:
14
diff
changeset
|
528 <test expect_num_outputs="1"> |
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
529 <param ftype="bam" name="input" value="in_test_11.bam" /> |
7
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
530 <conditional name="mode"> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
531 <conditional name="output_options"> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
532 <conditional name="output_format"> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
533 <param name="oformat" value="sam" /> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
534 <param name="with_header" value="true" /> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
535 </conditional> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
536 </conditional> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
537 </conditional> |
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
538 <output file="test_11.sam" ftype="sam" name="outputsam" lines_diff="2" /> |
0
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
539 </test> |
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
540 <!-- 12) --> |
15
6be888be75f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents:
14
diff
changeset
|
541 <test expect_num_outputs="1"> |
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
542 <param ftype="bam" name="input" value="in_test_11.bam" /> |
7
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
543 <conditional name="mode"> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
544 <param name="outtype" value="header" /> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
545 <conditional name="output_options"> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
546 <conditional name="output_format"> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
547 <param name="oformat" value="sam" /> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
548 </conditional> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
549 </conditional> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
550 </conditional> |
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
551 <output file="test_12.sam" ftype="sam" name="outputsam" lines_diff="2" /> |
0
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
552 </test> |
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
553 <!-- 13) --> |
15
6be888be75f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents:
14
diff
changeset
|
554 <test expect_num_outputs="1"> |
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
555 <param ftype="bam" name="input" value="in_test_11.bam" /> |
7
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
556 <conditional name="mode"> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
557 <conditional name="output_options"> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
558 <conditional name="output_format"> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
559 <param name="oformat" value="sam" /> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
560 <param name="with_header" value="false" /> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
561 </conditional> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
562 </conditional> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
563 </conditional> |
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
564 <output file="test_13.sam" ftype="sam" name="outputsam" lines_diff="2" /> |
0
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
565 </test> |
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
566 <!-- 14) count alignments --> |
15
6be888be75f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents:
14
diff
changeset
|
567 <test expect_num_outputs="1"> |
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
568 <param name="input" value="in_test_14.bam" ftype="bam" /> |
8
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
569 <conditional name="mode"> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
570 <param name="outtype" value="all_reads" /> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
571 <conditional name="output_options"> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
572 <param name="reads_report_type" value="count" /> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
573 </conditional> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
574 </conditional> |
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
575 <output name="outputcnt" file="test_14.tab" ftype="tabular" lines_diff="2" /> |
8
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
576 </test> |
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
577 <!-- 15) region filters --> |
15
6be888be75f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents:
14
diff
changeset
|
578 <test expect_num_outputs="1"> |
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
579 <param name="input" value="in_test_15.sam" ftype="sam" /> |
8
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
580 <conditional name="mode"> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
581 <param name="outtype" value="selected_reads" /> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
582 <section name="filter_config"> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
583 <conditional name="cond_region"> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
584 <param name="select_region" value="no"/> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
585 </conditional> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
586 </section> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
587 <conditional name="output_options"> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
588 <conditional name="output_format"> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
589 <param name="oformat" value="cram" /> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
590 </conditional> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
591 </conditional> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
592 </conditional> |
7
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
593 <conditional name="addref_cond"> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
594 <param name="addref_select" value="history" /> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
595 <param name="ref" value="test.fa" /> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
596 </conditional> |
16
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
15
diff
changeset
|
597 <output name="outputsam" file="test_15.cram" ftype="cram" compare="sim_size" delta="500" /> |
8
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
598 </test> |
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
599 <!-- 16) --> |
15
6be888be75f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents:
14
diff
changeset
|
600 <test expect_num_outputs="1"> |
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
601 <param name="input" value="in_test_14.bam" ftype="bam" /> |
8
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
602 <conditional name="mode"> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
603 <param name="outtype" value="selected_reads" /> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
604 <section name="filter_config"> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
605 <conditional name="cond_region"> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
606 <param name="select_region" value="no"/> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
607 </conditional> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
608 </section> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
609 <conditional name="output_options"> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
610 <conditional name="output_format"> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
611 <param name="oformat" value="cram" /> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
612 </conditional> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
613 </conditional> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
614 </conditional> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
615 <conditional name="addref_cond"> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
616 <param name="addref_select" value="history" /> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
617 <param name="ref" value="test.fa" /> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
618 </conditional> |
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
619 <output name="outputsam" file="test_15.cram" ftype="cram" compare="sim_size" delta="250" /> |
8
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
620 </test> |
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
621 <!-- 17) --> |
15
6be888be75f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents:
14
diff
changeset
|
622 <test expect_num_outputs="1"> |
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
623 <param name="input" value="in_test_17.cram" dbkey="equCab2" ftype="cram" /> |
8
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
624 <conditional name="mode"> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
625 <param name="outtype" value="selected_reads" /> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
626 <section name="filter_config"> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
627 <conditional name="cond_region"> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
628 <param name="select_region" value="no"/> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
629 </conditional> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
630 </section> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
631 <conditional name="output_options"> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
632 <conditional name="output_format"> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
633 <param name="oformat" value="bam" /> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
634 </conditional> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
635 </conditional> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
636 </conditional> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
637 <conditional name="addref_cond"> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
638 <param name="addref_select" value="cached" /> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
639 <param name="ref" value="equCab2chrM" /> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
640 </conditional> |
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
641 <output name="outputsam" file="test_17.bam" ftype="bam" lines_diff="4" /> |
8
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
642 </test> |
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
643 <!-- 18) --> |
15
6be888be75f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents:
14
diff
changeset
|
644 <test expect_num_outputs="1"> |
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
645 <param name="input" value="in_test_14.bam" ftype="bam" /> |
8
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
646 <conditional name="mode"> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
647 <param name="outtype" value="selected_reads" /> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
648 <section name="filter_config"> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
649 <conditional name="cond_region"> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
650 <param name="select_region" value="text"/> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
651 <param name="regions" value="CHROMOSOME_I" /> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
652 </conditional> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
653 </section> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
654 <conditional name="output_options"> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
655 <conditional name="output_format"> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
656 <param name="oformat" value="cram" /> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
657 </conditional> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
658 </conditional> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
659 </conditional> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
660 <conditional name="addref_cond"> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
661 <param name="addref_select" value="history" /> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
662 <param name="ref" value="test.fa" /> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
663 </conditional> |
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
664 <output name="outputsam" file="test_15.cram" ftype="cram" compare="sim_size" delta="250" /> |
7
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
665 </test> |
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
666 <!-- 19) --> |
15
6be888be75f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents:
14
diff
changeset
|
667 <test expect_num_outputs="1"> |
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
668 <param name="input" value="test_15.cram" ftype="cram" /> |
7
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
669 <conditional name="mode"> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
670 <param name="outtype" value="selected_reads" /> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
671 <section name="filter_config"> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
672 <conditional name="cond_region"> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
673 <param name="select_region" value="text"/> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
674 <param name="regions" value="CHROMOSOME_I" /> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
675 </conditional> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
676 </section> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
677 <conditional name="output_options"> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
678 <conditional name="output_format"> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
679 <param name="oformat" value="bam" /> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
680 </conditional> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
681 </conditional> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
682 </conditional> |
0
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
683 <conditional name="addref_cond"> |
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
684 <param name="addref_select" value="history" /> |
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
685 <param name="ref" value="test.fa" /> |
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
686 </conditional> |
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
687 <output name="outputsam" file="test_19.bam" ftype="bam" lines_diff="4"/> |
0
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
688 </test> |
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
689 <!-- 20) --> |
15
6be888be75f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents:
14
diff
changeset
|
690 <test expect_num_outputs="1"> |
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
691 <param name="input" value="test_15.cram" ftype="cram" /> |
7
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
692 <conditional name="mode"> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
693 <param name="outtype" value="selected_reads" /> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
694 <section name="filter_config"> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
695 <conditional name="cond_region"> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
696 <param name="select_region" value="bed" /> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
697 <param name="bedfile" value="test.bed" ftype="bed" /> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
698 </conditional> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
699 </section> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
700 <conditional name="output_options"> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
701 <conditional name="output_format"> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
702 <param name="oformat" value="bam" /> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
703 </conditional> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
704 </conditional> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
705 </conditional> |
0
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
706 <conditional name="addref_cond"> |
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
707 <param name="addref_select" value="history" /> |
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
708 <param name="ref" value="test.fa" /> |
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
709 </conditional> |
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
710 <output name="outputsam" file="test_20.bam" ftype="bam" lines_diff="4" /> |
0
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
diff
changeset
|
711 </test> |
14
5826298f6a73
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 5cb103832529f17e5c72e7f122758c13519fbe5e
iuc
parents:
13
diff
changeset
|
712 <!-- 21) sampling options target < total reads --> |
15
6be888be75f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents:
14
diff
changeset
|
713 <test expect_num_outputs="1"> |
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
714 <param name="input" value="in_test_15.sam" ftype="sam" /> |
7
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
715 <conditional name="mode"> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
716 <param name="outtype" value="selected_reads" /> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
717 <section name="subsample_config"> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
718 <conditional name="subsampling_mode"> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
719 <param name="select_subsample" value="target" /> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
720 <param name="target" value="2" /> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
721 </conditional> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
722 </section> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
723 <conditional name="output_options"> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
724 <conditional name="output_format"> |
8
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
725 <param name="oformat" value="input" /> |
7
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
726 </conditional> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
727 </conditional> |
2
02afb5ea2fce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
iuc
parents:
1
diff
changeset
|
728 </conditional> |
14
5826298f6a73
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 5cb103832529f17e5c72e7f122758c13519fbe5e
iuc
parents:
13
diff
changeset
|
729 <output name="outputsam" file="test_21.sam" ftype="sam" compare="diff" lines_diff="10" /> |
2
02afb5ea2fce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
iuc
parents:
1
diff
changeset
|
730 </test> |
14
5826298f6a73
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 5cb103832529f17e5c72e7f122758c13519fbe5e
iuc
parents:
13
diff
changeset
|
731 <!-- 22) target > total reads --> |
15
6be888be75f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents:
14
diff
changeset
|
732 <test expect_num_outputs="1"> |
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
733 <param name="input" value="in_test_15.sam" ftype="sam" /> |
7
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
734 <conditional name="mode"> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
735 <param name="outtype" value="selected_reads" /> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
736 <section name="subsample_config"> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
737 <conditional name="subsampling_mode"> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
738 <param name="select_subsample" value="target" /> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
739 <param name="target" value="20" /> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
740 </conditional> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
741 </section> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
742 <conditional name="output_options"> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
743 <conditional name="output_format"> |
8
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
744 <param name="oformat" value="input" /> |
7
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
745 </conditional> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
746 </conditional> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
747 </conditional> |
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
748 <output name="outputsam" file="test_22.sam" ftype="sam" lines_diff="2"/> |
7
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
749 </test> |
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
750 <!-- 23) --> |
15
6be888be75f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents:
14
diff
changeset
|
751 <test expect_num_outputs="1"> |
8
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
752 <!-- subsampling SAM input without reads --> |
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
753 <param name="input" value="in_test_23.sam" ftype="sam" /> |
8
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
754 <conditional name="mode"> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
755 <param name="outtype" value="selected_reads" /> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
756 <section name="subsample_config"> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
757 <conditional name="subsampling_mode"> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
758 <param name="select_subsample" value="target" /> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
759 <param name="target" value="20" /> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
760 </conditional> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
761 </section> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
762 <conditional name="output_options"> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
763 <conditional name="output_format"> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
764 <param name="oformat" value="input" /> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
765 </conditional> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
766 </conditional> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
767 </conditional> |
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
768 <output name="outputsam" file="test_23.sam" ftype="sam" lines_diff="2"/> |
8
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
769 </test> |
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
770 <!-- 24) --> |
15
6be888be75f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents:
14
diff
changeset
|
771 <test expect_num_outputs="1"> |
8
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
772 <!-- subsampling BAM input without reads --> |
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
773 <param name="input" value="in_test_24.bam" ftype="bam" /> |
8
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
774 <conditional name="mode"> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
775 <param name="outtype" value="selected_reads" /> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
776 <section name="subsample_config"> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
777 <conditional name="subsampling_mode"> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
778 <param name="select_subsample" value="target" /> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
779 <param name="target" value="20" /> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
780 </conditional> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
781 </section> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
782 <conditional name="output_options"> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
783 <conditional name="output_format"> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
784 <param name="oformat" value="input" /> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
785 </conditional> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
786 </conditional> |
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
787 </conditional> |
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
788 <output name="outputsam" file="test_24.bam" ftype="bam" lines_diff="2" /> |
8
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
789 </test> |
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
790 <!-- 25) --> |
15
6be888be75f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents:
14
diff
changeset
|
791 <test expect_num_outputs="1"> |
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
792 <param name="input" value="in_test_15.sam" ftype="sam" /> |
7
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
793 <conditional name="mode"> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
794 <param name="outtype" value="selected_reads" /> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
795 <section name="subsample_config"> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
796 <conditional name="subsampling_mode"> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
797 <param name="select_subsample" value="target" /> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
798 <param name="seed" value="7" /> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
799 <param name="target" value="2" /> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
800 </conditional> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
801 </section> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
802 <conditional name="output_options"> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
803 <conditional name="output_format"> |
8
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
804 <param name="oformat" value="input" /> |
7
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
805 </conditional> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
806 </conditional> |
2
02afb5ea2fce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
iuc
parents:
1
diff
changeset
|
807 </conditional> |
14
5826298f6a73
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 5cb103832529f17e5c72e7f122758c13519fbe5e
iuc
parents:
13
diff
changeset
|
808 <output name="outputsam" file="test_25.sam" ftype="sam" compare="diff" lines_diff="2" /> |
2
02afb5ea2fce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
iuc
parents:
1
diff
changeset
|
809 </test> |
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
810 <!-- 26) --> |
15
6be888be75f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents:
14
diff
changeset
|
811 <test expect_num_outputs="1"> |
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
812 <param name="input" value="in_test_14.bam" ftype="bam" /> |
7
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
813 <conditional name="mode"> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
814 <param name="outtype" value="selected_reads" /> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
815 <section name="subsample_config"> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
816 <conditional name="subsampling_mode"> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
817 <param name="select_subsample" value="target" /> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
818 <param name="seed" value="7" /> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
819 <param name="target" value="2" /> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
820 </conditional> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
821 </section> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
822 <conditional name="output_options"> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
823 <conditional name="output_format"> |
8
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
824 <param name="oformat" value="input" /> |
7
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
825 </conditional> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
826 </conditional> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
827 </conditional> |
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
828 <output name="outputsam" file="test_26.bam" ftype="bam" lines_diff="2" /> |
7
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
829 </test> |
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
830 <!-- 27) --> |
15
6be888be75f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents:
14
diff
changeset
|
831 <test expect_num_outputs="1"> |
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
832 <param name="input" value="in_test_14.bam" ftype="bam" /> |
7
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
833 <conditional name="mode"> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
834 <param name="outtype" value="selected_reads" /> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
835 <section name="subsample_config"> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
836 <conditional name="subsampling_mode"> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
837 <param name="select_subsample" value="target" /> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
838 <param name="seed" value="7" /> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
839 <param name="target" value="20" /> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
840 </conditional> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
841 </section> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
842 <conditional name="output_options"> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
843 <conditional name="output_format"> |
8
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
844 <param name="oformat" value="input" /> |
7
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
845 </conditional> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
846 </conditional> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
847 </conditional> |
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
848 <output name="outputsam" file="test_27.bam" ftype="bam" lines_diff="2"/> |
7
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
849 </test> |
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
850 <!-- 28) --> |
15
6be888be75f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents:
14
diff
changeset
|
851 <test expect_num_outputs="1"> |
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
852 <param name="input" value="in_test_14.bam" ftype="bam" /> |
7
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
853 <conditional name="mode"> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
854 <param name="outtype" value="selected_reads" /> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
855 <section name="subsample_config"> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
856 <conditional name="subsampling_mode"> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
857 <param name="select_subsample" value="fraction" /> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
858 <param name="seed" value="7" /> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
859 <param name="factor" value="5" /> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
860 </conditional> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
861 </section> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
862 <conditional name="output_options"> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
863 <conditional name="output_format"> |
8
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
864 <param name="oformat" value="input" /> |
7
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
865 </conditional> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
866 </conditional> |
2
02afb5ea2fce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
iuc
parents:
1
diff
changeset
|
867 </conditional> |
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
868 <output name="outputsam" file="test_28.bam" ftype="bam" lines_diff="2" /> |
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
869 </test> |
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
870 <!-- 29) --> |
15
6be888be75f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents:
14
diff
changeset
|
871 <test expect_num_outputs="1"> |
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
872 <param name="input" value="in_test_14.bam" ftype="bam" /> |
7
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
873 <conditional name="mode"> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
874 <param name="outtype" value="selected_reads" /> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
875 <section name="subsample_config"> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
876 <conditional name="subsampling_mode"> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
877 <param name="select_subsample" value="fraction" /> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
878 <param name="seed" value="7" /> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
879 <param name="factor" value="1.25" /> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
880 </conditional> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
881 </section> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
882 <conditional name="output_options"> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
883 <param name="reads_report_type" value="dropped" /> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
884 <conditional name="output_format"> |
8
bf328cec6a42
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e73e642259254253f71335ed1cbd738bb06d3346"
iuc
parents:
7
diff
changeset
|
885 <param name="oformat" value="input" /> |
7
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
886 </conditional> |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
887 </conditional> |
2
02afb5ea2fce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
iuc
parents:
1
diff
changeset
|
888 </conditional> |
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
889 <output name="outputsam" file="test_29.bam" ftype="bam" lines_diff="2"/> |
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
890 </test> |
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
891 <!-- 30) testing tag filtering --> |
15
6be888be75f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents:
14
diff
changeset
|
892 <test expect_num_outputs="1"> |
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
893 <param name="input" value="in_test_30.bam" ftype="bam" /> |
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
894 <conditional name="mode"> |
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
895 <param name="outtype" value="selected_reads" /> |
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
896 <section name="filter_config"> |
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
897 <param name="tag" value="XS:-18" /> |
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
898 </section> |
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
899 <conditional name="output_options"> |
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
900 <conditional name="output_format"> |
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
901 <param name="oformat" value="bam" /> |
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
902 </conditional> |
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
903 </conditional> |
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
904 </conditional> |
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
905 <assert_command> |
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
906 <has_text text="--tag 'XS:-18'"/> |
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
907 </assert_command> |
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
908 <output name="outputsam" file="test_30.bam" ftype="bam" lines_diff="2" /> |
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
909 </test> |
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
910 <!-- 31) testing readname filtering --> |
15
6be888be75f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit cd62639660bef041ba14ecff337fb98e84e75d8a
iuc
parents:
14
diff
changeset
|
911 <test expect_num_outputs="1"> |
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
912 <param name="input" value="in_test_30.bam" ftype="bam" /> |
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
913 <conditional name="mode"> |
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
914 <param name="outtype" value="selected_reads" /> |
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
915 <section name="filter_config"> |
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
916 <param name="qname_file" value="readnames.txt" /> |
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
917 </section> |
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
918 <conditional name="output_options"> |
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
919 <conditional name="output_format"> |
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
920 <param name="oformat" value="bam" /> |
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
921 </conditional> |
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
922 </conditional> |
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
923 </conditional> |
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
924 <assert_command> |
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
925 <has_text text="--qname-file"/> |
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
926 </assert_command> |
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
927 <output name="outputsam" file="test_31.bam" ftype="bam" lines_diff="2" /> |
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
928 </test> |
16
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
15
diff
changeset
|
929 <!-- 32) testing expression filters --> |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
15
diff
changeset
|
930 <test expect_num_outputs="1"> |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
15
diff
changeset
|
931 <param name="input" value="in_test_30.bam" ftype="bam"/> |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
15
diff
changeset
|
932 <conditional name="mode"> |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
15
diff
changeset
|
933 <param name="outtype" value="selected_reads" /> |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
15
diff
changeset
|
934 <section name="filter_config"> |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
15
diff
changeset
|
935 <conditional name="cond_expr"> |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
15
diff
changeset
|
936 <param name="select_expr" value="yes"/> |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
15
diff
changeset
|
937 <param name="expression" value="sclen>0"/> |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
15
diff
changeset
|
938 </conditional> |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
15
diff
changeset
|
939 </section> |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
15
diff
changeset
|
940 <conditional name="output_options"> |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
15
diff
changeset
|
941 <conditional name="output_format"> |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
15
diff
changeset
|
942 <param name="oformat" value="bam" /> |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
15
diff
changeset
|
943 </conditional> |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
15
diff
changeset
|
944 </conditional> |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
15
diff
changeset
|
945 </conditional> |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
15
diff
changeset
|
946 <assert_command> |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
15
diff
changeset
|
947 <has_text text="-e 'sclen>0'"/> |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
15
diff
changeset
|
948 </assert_command> |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
15
diff
changeset
|
949 <output name="outputsam" file="test_32.bam" ftype="bam" lines_diff="2" /> |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
15
diff
changeset
|
950 </test> |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
15
diff
changeset
|
951 <!-- 33) testing expression filters --> |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
15
diff
changeset
|
952 <test expect_num_outputs="1"> |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
15
diff
changeset
|
953 <param name="input" value="in_test_30.bam" ftype="bam"/> |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
15
diff
changeset
|
954 <conditional name="mode"> |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
15
diff
changeset
|
955 <param name="outtype" value="selected_reads" /> |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
15
diff
changeset
|
956 <section name="filter_config"> |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
15
diff
changeset
|
957 <conditional name="cond_expr"> |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
15
diff
changeset
|
958 <param name="select_expr" value="yes"/> |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
15
diff
changeset
|
959 <param name="expression" value='rname!="chr13"'/> |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
15
diff
changeset
|
960 </conditional> |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
15
diff
changeset
|
961 </section> |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
15
diff
changeset
|
962 <conditional name="output_options"> |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
15
diff
changeset
|
963 <conditional name="output_format"> |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
15
diff
changeset
|
964 <param name="oformat" value="bam" /> |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
15
diff
changeset
|
965 </conditional> |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
15
diff
changeset
|
966 </conditional> |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
15
diff
changeset
|
967 </conditional> |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
15
diff
changeset
|
968 <assert_command> |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
15
diff
changeset
|
969 <has_text text="-e 'rname!="/> |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
15
diff
changeset
|
970 </assert_command> |
2dce91e11ca7
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971 <output name="outputsam" file="test_33.bam" ftype="bam" lines_diff="2" /> |
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972 </test> |
0
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973 </tests> |
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974 <help> |
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975 **What it does** |
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976 |
10
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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977 Samtools view can: |
0
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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978 |
7
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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979 1. convert between alignment formats (SAM, BAM, CRAM) |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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980 2. filter and subsample alignments according to user-specified criteria |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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981 3. count the reads in the input dataset or those retained after filtering |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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982 and subsampling |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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983 4. obtain just the header of the input in any supported format |
10
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984 |
7
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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985 In addition, the tool has (limited) options to modify read records during conversion and/or filtering by: |
0
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986 |
7
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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987 - stripping them of user-specified tags |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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988 - collapsing backward CIGAR operations if they are specified in their CIGAR |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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989 fields |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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990 |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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991 With default settings, the tool generates a BAM dataset with the header and |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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992 reads found in the input dataset (which can be in SAM, BAM, or CRAM format). |
0
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993 |
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994 **Alignment format conversion** |
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995 |
7
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996 By changing the *Output format* it is possible to convert an input dataset to |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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997 another format. |
10
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998 Inputs of type SAM, BAM, and CRAM are accepted and can be converted to each of these formats (alternatively alignment counts can be computed) by selecting the appropriate "Output type". |
0
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999 |
10
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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1000 .. class:: infomark |
0
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1001 |
7
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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1002 The tool allows you to specify a reference sequence. This is required for SAM input with missing @SQ headers (which include sequence names, length, md5, etc) and useful (and sometimes necessary) for CRAM input and output. In the following the use of the reference sequence in the CRAM format is detailed. |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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1003 CRAM is (primarily) a reference-based compressed format, i.e. only sequence differences between aligned reads and the reference are stored. As a consequence, the reference that was used during read mapping is needed in order to interpret the alignment records (a checksum stored in the CRAM file is used to verify that only the correct reference sequence can be used). This allows for more space-efficient storage than with BAM format, but such a CRAM file is not usable without its reference. |
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1004 It is also possible, however, to use CRAM without a reference with the disadvantage that the reference sequence gets stored then explicitely (as in SAM and BAM). |
0
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1005 |
1
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1006 The Galaxy tool **currently generates only CRAM without reference sequence**. |
0
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1007 |
1
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1008 For reference based CRAM input the correct refernce sequence needs to be specified. |
0
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1009 |
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1010 **Filtering alignments** |
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1011 |
7
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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1012 If you ask for *A filtered/subsampled selection of reads*, the tool will allow |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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1013 you to specify filter conditions and/or to choose a subsampling strategy, and |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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1014 the output will contain one of the following depending on your choice under |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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1015 *What would you like to have reported?*: |
0
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1016 |
7
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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1017 - All reads retained after filtering and subsampling |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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1018 - Reads dropped during filtering and subsampling |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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1019 |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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1020 If instead you want to *split* the input reads based on your criteria and |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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1021 obtain *two* datasets, one with the retained and one with the dropped reads, check |
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1022 the *Produce extra dataset with dropped/retained reads?* option. |
0
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1023 |
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1024 |
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1025 **Filtering by regions** |
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1026 |
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1027 You may specify one or more space-separated region specifications after the input filename to restrict output to only those alignments which overlap the specified region(s). Use of region specifications requires a coordinate-sorted and indexed input file (in BAM or CRAM format). |
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1028 |
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1029 Regions can be specified as: RNAME[:STARTPOS[-ENDPOS]] and all position coordinates are 1-based. |
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1030 |
7
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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1031 .. class:: Warning mark |
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1032 |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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1033 When multiple regions are given, some alignments may be output multiple times if they overlap more than one of the specified regions. |
0
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1034 |
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1035 Examples of region specifications: |
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1036 |
7
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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1037 ``chr1`` |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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1038 Output all alignments mapped to the reference sequence named 'chr1' (i.e. @SQ SN:chr1). |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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|
1039 |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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1040 ``chr2:1000000`` |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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1041 The region on chr2 beginning at base position 1,000,000 and ending at the end of the chromosome. |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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1042 |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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1043 ``chr3:1000-2000`` |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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1044 The 1001bp region on chr3 beginning at base position 1,000 and ending at base position 2,000 (including both end positions). |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
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|
1045 |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
1046 ``*`` |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
1047 Output the unmapped reads at the end of the file. (This does not include any unmapped reads placed on a reference sequence alongside their mapped mates.) |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
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diff
changeset
|
1048 |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
1049 ``.`` |
b01db2684fa5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 6692949aa694102abb64c67d46196a822fcb61bf"
iuc
parents:
6
diff
changeset
|
1050 Output all alignments. (Mostly unnecessary as not specifying a region at all has the same effect.) |
0
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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parents:
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changeset
|
1051 |
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
iuc
parents:
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changeset
|
1052 **Filtering by quality** |
00d1f08bdcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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changeset
|
1053 |
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
1054 This filters based on the MAPQ column of the SAM format which gives an estimate about the correct placement of the alignment. Note that aligners do not follow a consistent definition. |
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
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changeset
|
1055 |
16
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
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diff
changeset
|
1056 **Filtering by Tag** |
10
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
1057 |
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
1058 This filter allows to select reads based on tool or user specific tags, e.g., XS:i:-18 the alignment score tag of bowtie. |
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
1059 Thus to filter for a specific value of the tag you need the format STR1:STR2, e.g., XS:-18 to filter reads with an aligment score of -18. |
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
iuc
parents:
9
diff
changeset
|
1060 You can also just write STR1 without the value STR2 hence the filter selects all reads with the tag STR1, e.g., XS. |
350bbc5c2ffd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
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changeset
|
1061 |
16
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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15
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changeset
|
1062 **Filtering by Expression** |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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diff
changeset
|
1063 |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
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15
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changeset
|
1064 |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
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15
diff
changeset
|
1065 Filter expressions are used as an on-the-fly checking of incoming SAM, BAM or CRAM records, discarding records that do not match the specified expression. |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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changeset
|
1066 |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
15
diff
changeset
|
1067 The language used is primarily C style, but with a few differences in the precedence rules for bit operators and the inclusion of regular expression |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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diff
changeset
|
1068 matching. |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
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diff
changeset
|
1069 |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
15
diff
changeset
|
1070 The operator precedence, from strongest binding to weakest, is |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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|
1071 |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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|
1072 :: |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
15
diff
changeset
|
1073 |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
15
diff
changeset
|
1074 Grouping (, ) E.g. "(1+2)*3" |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
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diff
changeset
|
1075 Values: literals, vars Numbers, strings and variables |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
15
diff
changeset
|
1076 Unary ops: +, -, !, ~ E.g. -10 +10, !10 (not), ~5 (bit not) |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
15
diff
changeset
|
1077 Math ops: \*, /, % Multiply, division and (integer) modulo |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
15
diff
changeset
|
1078 Math ops: +, - Addition / subtraction |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
15
diff
changeset
|
1079 Bit-wise: & Integer AND |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
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|
1080 Bit-wise ^ Integer XOR |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
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diff
changeset
|
1081 Bit-wise | Integer OR |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
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|
1082 Conditionals: >, >=, <, <= |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
15
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|
1083 Equality: \=\=, !=, =~, !~ =~ and !~ match regular expressions |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
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|
1084 Boolean: &&, || Logical AND / OR |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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|
1085 |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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diff
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|
1086 |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
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diff
changeset
|
1087 Expressions are computed using floating point mathematics, so "10 / 4" evaluates to 2.5 rather than 2. They may be written as integers in decimal or |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
parents:
15
diff
changeset
|
1088 "0x" plus hexadecimal, and floating point with or without exponents.However operations that require integers first do an implicit type conversion, so |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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parents:
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diff
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|
1089 "7.9 % 5" is 2 and "7.9 & 4.1" is equivalent to "7 & 4", which is 4. Strings are always specified using double quotes. To get a double quote in a |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
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changeset
|
1090 string, use backslash. Similarly a double backslash is used to get a literal backslash. For example ab\"c\\d is the string ab"c\d. |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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diff
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|
1091 |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
iuc
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|
1092 Comparison operators are evaluated as a match being 1 and a mismatch being 0, thus "(2 > 1) + (3 < 5)" evaluates as 2. All comparisons involving undefined (null) values are deemed to be false. |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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|
1093 |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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|
1094 The variables are where the file format specifics are accessed from the expression. The variables correspond to SAM fields, for example to find paired |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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|
1095 alignments with high mapping quality and a very large insert size, we may use the expression "mapq >= 30 && (tlen >= 100000 || tlen <= -100000)". Valid |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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|
1096 variable names and their data types are: |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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|
1097 |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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|
1098 :: |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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|
1099 |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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|
1100 endpos int Alignment end position (1-based) |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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|
1101 flag int Combined FLAG field |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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1102 flag.paired int Single bit, 0 or 1 |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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1103 flag.proper_pair int Single bit, 0 or 2 |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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1104 flag.unmap int Single bit, 0 or 4 |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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1105 flag.munmap int Single bit, 0 or 8 |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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1106 flag.reverse int Single bit, 0 or 16 |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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1107 flag.mreverse int Single bit, 0 or 32 |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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1108 flag.read1 int Single bit, 0 or 64 |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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1109 flag.read2 int Single bit, 0 or 128 |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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1110 flag.secondary int Single bit, 0 or 256 |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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1111 flag.qcfail int Single bit, 0 or 512 |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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1112 flag.dup int Single bit, 0 or 1024 |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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1113 flag.supplementary int Single bit, 0 or 2048 |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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1114 hclen int Number of hard-clipped bases |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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1115 library string Library (LB header via RG) |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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1116 mapq int Mapping quality |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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1117 mpos int Synonym for pnext |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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1118 mrefid int Mate reference number (0 based) |
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1119 mrname string Synonym for rnext |
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1120 ncigar int Number of cigar operations |
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1121 pnext int Mate's alignment position (1-based) |
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1122 pos int Alignment position (1-based) |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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1123 qlen int Alignment length: no. query bases |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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1124 qname string Query name |
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1125 qual string Quality values (raw, 0 based) |
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1126 refid int Integer reference number (0 based) |
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1127 rlen int Alignment length: no. reference bases |
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1128 rname string Reference name |
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1129 rnext string Mate's reference name |
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1130 sclen int Number of soft-clipped bases |
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1131 seq string Sequence |
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1132 tlen int Template length (insert size) |
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1133 [XX] int / string XX tag value |
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1134 |
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1135 |
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1136 Flags are returned either as the whole flag value or by checking for a single bit. Hence the filter expression flag.dup is equivalent to flag & 1024. |
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1137 |
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1138 "qlen" and "rlen" are measured using the CIGAR string to count the number of query (sequence) and reference bases consumed. Note "qlen" may not exactly |
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1139 match the length of the "seq" field if the sequence is "*". |
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1140 |
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1141 "sclen" and "hclen" are the number of soft and hard-clipped bases respectively. The formula "qlen-sclen" gives the number of sequence bases used in the |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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1142 alignment, distinguishing between global alignment and local alignment length. |
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1143 |
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1144 "endpos" is the (1-based inclusive) position of the rightmost mapped base of the read, as measured using the CIGAR string, and for mapped reads is |
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1145 equivalent to "pos+rlen-1". For unmapped reads, it is the same as "pos". |
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1146 |
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1147 Reference names may be matched either by their string forms ("rname" and "mrname") or as the Nth @SQ line (counting from zero) as stored in BAM using |
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1148 "tid" and "mtid" respectively. |
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1149 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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1150 Auxiliary tags are described in square brackets and these expand to either integer or string as defined by the tag itself (XX:Z:string or XX:i:int). |
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1151 For example [NM]>=10 can be used to look for alignments with many mismatches and [RG]=~"grp[ABC]-" will match the read-group string. |
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1152 |
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1153 If no comparison is used with an auxiliary tag it is taken simply to be a test for the existence of that tag. So [NM] will return any record containing |
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1154 an NM tag, even if that tag is zero (NM:i:0). In htslib <= 1.15 negating this with ![NM] gave misleading results as it was true if the tag did not exist |
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1155 or did exist but was zero. Now this is strictly does-not-exist. An explicit exists([NM]) and !exists([NM]) function has also been added to make |
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1156 this intention clear. |
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1157 |
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1158 Similarly in htslib <= 1.15 using [NM]!=0 was true both when the tag existed and was not zero as well as when the tag did not exist. From 1.16 onwards |
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1159 all comparison operators are only true for tags that exist, so [NM]!=0 works as expected. |
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1160 |
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1161 Some simple functions are available to operate on strings. These treat the strings as arrays of bytes, permitting their length, minimum, maximum and |
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1162 average values to be computed. These are useful for processing Quality Scores. |
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1163 |
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1164 :: |
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1165 |
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1166 length(x) Length of the string (excluding nul char) |
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1167 min(x) Minimum byte value in the string |
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1168 max(x) Maximum byte value in the string |
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1169 avg(x) Average byte value in the string |
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1170 |
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1171 |
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1172 Note that "avg" is a floating point value and it may be NAN for empty strings. This means that "avg(qual)" does not produce an error for records that |
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1173 have both seq and qual of "*". NAN values will fail any conditional checks, so e.g. "avg(qual) > 20" works and will not report these records. NAN also |
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1174 fails all equality, < and > comparisons, and returns zero when given as an argument to the exists function. It can be negated with !x in which case it |
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1175 becomes true. |
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1176 |
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1177 Functions that operate on both strings and numerics: |
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1178 |
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1179 :: |
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1180 |
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1181 exists(x) True if the value exists (or is explicitly true). |
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1182 default(x,d) Value x if it exists or d if not. |
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1183 |
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1184 Functions that apply only to numeric values: |
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1185 |
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1186 :: |
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1187 |
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1188 qrt(x) Square root of x |
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1189 og(x) Natural logarithm of x |
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1190 ow(x, y) Power function, x to the power of y |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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1191 xp(x) Base-e exponential, equivalent to pow(e,x) |
2dce91e11ca7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
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1192 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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1193 </help> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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1194 <expand macro="citations"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
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1195 </tool> |