Mercurial > repos > devteam > samtools_sort
annotate macros.xml @ 2:f56bdb93ae58 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
author | iuc |
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date | Wed, 19 Sep 2018 09:53:49 -0400 |
parents | cab3f8d35989 |
children | e613c1ad4c4c |
rev | line source |
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0 | 1 <macros> |
2 <xml name="requirements"> | |
3 <requirements> | |
2
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
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4 <requirement type="package" version="@TOOL_VERSION@">samtools</requirement> |
0 | 5 <yield/> |
6 </requirements> | |
7 </xml> | |
2
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
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8 <token name="@TOOL_VERSION@">1.9</token> |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
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9 <token name="@FLAGS@">#set $flags = sum(map(int, str($filter).split(',')))</token> |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
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10 <token name="@PREPARE_IDX@"><![CDATA[ |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
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11 ##prepare input and indices |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
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12 ln -s '$input' infile && |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
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13 #if $input.is_of_type('bam'): |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
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14 #if str( $input.metadata.bam_index ) != "None": |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
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15 ln -s '${input.metadata.bam_index}' infile.bai && |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
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16 #else: |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
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17 samtools index infile infile.bai && |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
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18 #end if |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
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19 #elif $input.is_of_type('cram'): |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
parents:
1
diff
changeset
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20 #if str( $input.metadata.cram_index ) != "None": |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
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21 ln -s '${input.metadata.cram_index}' infile.crai && |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
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22 #else: |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
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changeset
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23 samtools index infile infile.crai && |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
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24 #end if |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
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changeset
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25 #end if |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
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26 ]]></token> |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
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27 <token name="@PREPARE_IDX_MULTIPLE@"><![CDATA[ |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
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changeset
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28 ##prepare input and indices |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
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29 #for $i, $bam in enumerate( $input_bams ): |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
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30 ln -s '$bam' '${i}' && |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
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31 #if $bam.is_of_type('bam'): |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
parents:
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32 #if str( $bam.metadata.bam_index ) != "None": |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
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33 ln -s '${bam.metadata.bam_index}' '${i}.bai' && |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
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34 #else: |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
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35 samtools index '${i}' '${i}.bai' && |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
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36 #end if |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
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37 #elif $bam.is_of_type('cram'): |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
parents:
1
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changeset
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38 #if str( $bam.metadata.cram_index ) != "None": |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
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diff
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39 ln -s '${bam.metadata.cram_index}' '${i}.crai' && |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
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40 #else: |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
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41 samtools index '${i}' '${i}.crai' && |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
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42 #end if |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
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43 #end if |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
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44 #end for |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
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45 ]]></token> |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
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46 <token name="@PREPARE_FASTA_IDX@"><![CDATA[ |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
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47 ##checks for reference data ($addref_cond.addref_select=="history" or =="cached") |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
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48 ##and sets the -t/-T parameters accordingly: |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
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49 ##- in case of history a symbolic link is used because samtools (view) will generate |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
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50 ## the index which might not be possible in the directory containing the fasta file |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
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51 ##- in case of cached the absolute path is used which allows to read the cram file |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
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52 ## without specifying the reference |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
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53 #if $addref_cond.addref_select == "history": |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
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54 ln -s '${addref_cond.ref}' reference.fa && |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
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55 samtools faidx reference.fa && |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
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56 #set reffa=str($addref_cond.ref) |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
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57 #set reffai="reference.fa.fai" |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
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58 #elif $addref_cond.addref_select == "cached": |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
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59 #set reffa=str($addref_cond.ref.fields.path) |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
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60 #set reffai=str($addref_cond.ref.fields.path) |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
iuc
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61 #else |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
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62 #set reffa=None |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
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63 #set reffai=None |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
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64 #end if |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
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65 ]]></token> |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
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66 <token name="@ADDTHREADS@"><![CDATA[ |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
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67 ##compute the number of ADDITIONAL threads to be used by samtools (-@) |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
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68 addthreads=\${GALAXY_SLOTS:-1} && (( addthreads-- )) && |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
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69 ]]></token> |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
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70 |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
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71 <token name="@ADDMEMORY@"><![CDATA[ |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
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72 ##compute the number of memory available to samtools sort (-m) |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
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73 ##use only 75% of available: https://github.com/samtools/samtools/issues/831 |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
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74 addmemory=\${GALAXY_MEMORY_MB_PER_SLOT:-768} && |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
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75 ((addmemory=addmemory*75/100)) && |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
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76 ]]></token> |
f56bdb93ae58
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
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77 <xml name="flag_options"> |
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78 <option value="1">read is paired</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
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79 <option value="2">read is mapped in a proper pair</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
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80 <option value="4">read is unmapped</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
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81 <option value="8">mate is unmapped</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
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82 <option value="16">read reverse strand</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
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83 <option value="32">mate reverse strand</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
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84 <option value="64">read is the first in a pair</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
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85 <option value="128">read is the second in a pair</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
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86 <option value="256">alignment or read is not primary</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
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87 <option value="512">read fails platform/vendor quality checks</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
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88 <option value="1024">read is a PCR or optical duplicate</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
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89 <option value="2048">supplementary alignment</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9f6dd28ae31897068c9f8b5d842750d5d7cd600c
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90 </xml> |
0 | 91 <xml name="citations"> |
92 <citations> | |
93 <citation type="bibtex"> | |
94 @misc{SAM_def, | |
95 title={Definition of SAM/BAM format}, | |
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96 url = {https://samtools.github.io/hts-specs/},} |
0 | 97 </citation> |
98 <citation type="doi">10.1093/bioinformatics/btp352</citation> | |
99 <citation type="doi">10.1093/bioinformatics/btr076</citation> | |
100 <citation type="doi">10.1093/bioinformatics/btr509</citation> | |
101 <citation type="bibtex"> | |
102 @misc{Danecek_et_al, | |
103 Author={Danecek, P., Schiffels, S., Durbin, R.}, | |
104 title={Multiallelic calling model in bcftools (-m)}, | |
105 url = {http://samtools.github.io/bcftools/call-m.pdf},} | |
106 </citation> | |
107 <citation type="bibtex"> | |
108 @misc{Durbin_VCQC, | |
109 Author={Durbin, R.}, | |
110 title={Segregation based metric for variant call QC}, | |
111 url = {http://samtools.github.io/bcftools/rd-SegBias.pdf},} | |
112 </citation> | |
113 <citation type="bibtex"> | |
114 @misc{Li_SamMath, | |
115 Author={Li, H.}, | |
116 title={Mathematical Notes on SAMtools Algorithms}, | |
117 url = {http://www.broadinstitute.org/gatk/media/docs/Samtools.pdf},} | |
118 </citation> | |
119 <citation type="bibtex"> | |
120 @misc{SamTools_github, | |
121 title={SAMTools GitHub page}, | |
122 url = {https://github.com/samtools/samtools},} | |
123 </citation> | |
124 </citations> | |
125 </xml> | |
126 <xml name="version_command"> | |
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127 <version_command><![CDATA[samtools 2>&1 | grep Version]]></version_command> |
0 | 128 </xml> |
129 <xml name="stdio"> | |
130 <stdio> | |
131 <exit_code range="1:" level="fatal" description="Error" /> | |
132 </stdio> | |
133 </xml> | |
134 </macros> |