Mercurial > repos > iuc > samtools_bam_to_cram
annotate samtools_bam_to_cram.xml @ 0:b5dc4f88fb2d draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_cram commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
author | iuc |
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date | Tue, 09 May 2017 11:18:16 -0400 |
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children | 3e15f2544a5c |
rev | line source |
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0
b5dc4f88fb2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_cram commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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1 <tool id="samtools_bam_to_cram" name="samtools BAM to CRAM" version="@TOOL_VERSION@"> |
b5dc4f88fb2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_cram commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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2 <description>convert BAM alignments to CRAM format</description> |
b5dc4f88fb2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_cram commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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3 |
b5dc4f88fb2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_cram commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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4 <macros> |
b5dc4f88fb2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_cram commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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5 <import>macros.xml</import> |
b5dc4f88fb2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_cram commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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6 </macros> |
b5dc4f88fb2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_cram commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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7 <expand macro="requirements"/> |
b5dc4f88fb2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_cram commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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8 <expand macro="stdio"/> |
b5dc4f88fb2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_cram commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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9 <expand macro="version_command"/> |
b5dc4f88fb2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_cram commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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10 |
b5dc4f88fb2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_cram commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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11 <command><![CDATA[ |
b5dc4f88fb2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_cram commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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12 #if str( $input_alignment.metadata.bam_index ) != "None": |
b5dc4f88fb2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_cram commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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13 ln |
b5dc4f88fb2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_cram commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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14 -f |
b5dc4f88fb2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_cram commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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15 -s |
b5dc4f88fb2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_cram commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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16 '${input_alignment.metadata.bam_index}' |
b5dc4f88fb2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_cram commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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17 '${input_alignment}.bai' |
b5dc4f88fb2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_cram commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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18 && |
b5dc4f88fb2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_cram commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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19 #end if |
b5dc4f88fb2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_cram commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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20 |
b5dc4f88fb2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_cram commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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21 #if $reference_source.reference_source_selector == 'history': |
b5dc4f88fb2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_cram commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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22 #set ref_fa = 'ref.fa' |
b5dc4f88fb2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_cram commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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23 ln -s '${reference_source.input_reference}' ref.fa && |
b5dc4f88fb2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_cram commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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24 #else: |
b5dc4f88fb2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_cram commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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25 #set ref_fa = str( $reference_source.input_reference.fields.path ) |
b5dc4f88fb2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_cram commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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26 #end if |
b5dc4f88fb2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_cram commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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27 |
b5dc4f88fb2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_cram commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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28 samtools view |
b5dc4f88fb2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_cram commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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29 #if $parameter_regions.target_region == "regions_bed_file" |
b5dc4f88fb2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_cram commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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30 -L '${parameter_regions.regions_bed_file}' |
b5dc4f88fb2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_cram commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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31 #end if |
b5dc4f88fb2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_cram commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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32 |
b5dc4f88fb2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_cram commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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33 -@\${GALAXY_SLOTS:-1} |
b5dc4f88fb2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_cram commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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34 -C |
b5dc4f88fb2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_cram commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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35 -T '$ref_fa' |
b5dc4f88fb2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_cram commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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36 -o '${output_alignment}' |
b5dc4f88fb2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_cram commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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37 |
b5dc4f88fb2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_cram commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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38 '${input_alignment}' |
b5dc4f88fb2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_cram commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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39 |
b5dc4f88fb2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_cram commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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40 #if $parameter_regions.target_region == "region" |
b5dc4f88fb2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_cram commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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41 '${parameter_regions.region_string}' |
b5dc4f88fb2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_cram commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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42 #end if |
b5dc4f88fb2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_cram commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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43 ]]></command> |
b5dc4f88fb2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_cram commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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44 |
b5dc4f88fb2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_cram commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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45 <inputs> |
b5dc4f88fb2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_cram commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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46 <param name="input_alignment" type="data" format="bam,sam" label="BAM (or SAM) alignment file"/> |
b5dc4f88fb2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_cram commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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47 <conditional name="reference_source"> |
b5dc4f88fb2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_cram commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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48 <param name="reference_source_selector" type="select" label="Load reference genome from"> |
b5dc4f88fb2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_cram commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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49 <option value="cached">Local cache</option> |
b5dc4f88fb2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_cram commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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50 <option value="history">History</option> |
b5dc4f88fb2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_cram commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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51 </param> |
b5dc4f88fb2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_cram commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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52 <when value="cached"> |
b5dc4f88fb2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_cram commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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53 <param name="input_reference" type="select" label="Reference genome"> |
b5dc4f88fb2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_cram commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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54 <options from_data_table="fasta_indexes"> |
b5dc4f88fb2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_cram commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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55 <filter type="data_meta" ref="input_alignment" key="dbkey" column="1" /> |
b5dc4f88fb2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_cram commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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56 </options> |
b5dc4f88fb2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_cram commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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57 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> |
b5dc4f88fb2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_cram commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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58 </param> |
b5dc4f88fb2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_cram commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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59 </when> |
b5dc4f88fb2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_cram commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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60 <when value="history"> |
b5dc4f88fb2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_cram commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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61 <param name="input_reference" type="data" format="fasta" label="Reference FASTA file"/> |
b5dc4f88fb2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_cram commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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62 </when> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_cram commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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63 </conditional> |
b5dc4f88fb2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_cram commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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64 <conditional name="parameter_regions"> |
b5dc4f88fb2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_cram commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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65 <param name="target_region" type="select" label="Choose conversion within specific genomic region(s)"> |
b5dc4f88fb2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_cram commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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66 <option value="entire_input_file">Entire BAM alignment file</option> |
b5dc4f88fb2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_cram commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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67 <option value="region">Specific region</option> |
b5dc4f88fb2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_cram commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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68 <option value="regions_bed_file">List of specific regions (BED file)</option> |
b5dc4f88fb2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_cram commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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69 </param> |
b5dc4f88fb2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_cram commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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70 <when value="entire_input_file" /> |
b5dc4f88fb2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_cram commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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71 <when value="region"> |
b5dc4f88fb2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_cram commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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72 <param name="region_string" type="text" label="Samtools: region in which pileup is generated" help="e.g. chrX or chr:start-end" /> |
b5dc4f88fb2d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_cram commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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73 </when> |
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74 <when value="regions_bed_file"> |
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75 <param name="regions_bed_file" argument="-L" type="data" format="bed" |
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76 label="Only include reads overlapping this BED file" /> |
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77 </when> |
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78 </conditional> |
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79 </inputs> |
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80 |
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81 <outputs> |
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82 <data name="output_alignment" format="cram" label="$tool.name on ${on_string}.cram"></data> |
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83 </outputs> |
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84 |
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85 <tests> |
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86 <test> |
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87 <param name="input_alignment" value="test.bam" ftype="bam" /> |
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88 <param name="reference_source_selector" value="history" /> |
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89 <param name="input_reference" value="test.fa" /> |
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90 <param name="target_region" value="entire_input_file" /> |
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91 |
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92 <output name="output_alignment" file="test.cram" compare="sim_size" delta="250" /> |
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93 </test> |
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94 <test> |
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95 <param name="input_alignment" value="test.sam" ftype="sam" /> |
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96 <param name="reference_source_selector" value="history" /> |
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97 <param name="input_reference" value="test.fa" /> |
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98 <param name="target_region" value="entire_input_file" /> |
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99 |
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100 <output name="output_alignment" file="test.cram" compare="sim_size" delta="250" /> |
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101 </test> |
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102 <test> |
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103 <param name="input_alignment" value="test.bam" ftype="bam" /> |
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104 <param name="reference_source_selector" value="history" /> |
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105 <param name="input_reference" value="test.fa" /> |
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106 <param name="target_region" value="region" /> |
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107 <param name="region_string" value="CHROMOSOME_I" /> |
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108 |
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109 <output name="output_alignment" file="test.cram" compare="sim_size" delta="250" /> |
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110 </test> |
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111 <test> |
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112 <param name="input_alignment" value="test.bam" ftype="bam" /> |
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113 <param name="reference_source_selector" value="history" /> |
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114 <param name="input_reference" value="test.fa" /> |
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115 <param name="target_region" value="regions_bed_file" /> |
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116 <param name="regions_bed_file" value="test.bed" ftype="bed" /> |
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117 |
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118 <output name="output_alignment" file="test.cram" compare="sim_size" delta="250" /> |
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119 </test> |
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120 <test> |
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121 <param name="input_alignment" ftype="bam" dbkey="equCab2" value="sam_to_bam_out2.bam" /> |
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122 <param name="reference_source_selector" value="cached" /> |
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123 <param name="input_reference" value="equCab2chrM" /> |
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124 <param name="target_region" value="entire_input_file" /> |
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125 <output name="output_alignment" file="test2.cram" compare="sim_size" delta="250" /> |
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126 </test> |
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127 </tests> |
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128 |
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129 <help><![CDATA[ |
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130 **What this tool does** |
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131 |
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132 Converts alignments from the BAM format to the CRAM format using the ``samtools view`` command. |
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133 The CRAM format does additional compression relative to the reference genome which makes the compression in terms of file size more efficient. |
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134 ]]></help> |
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135 |
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136 <expand macro="citations" /> |
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137 </tool> |