Mercurial > repos > iuc > multiqc
comparison multiqc.xml @ 1:6999173dc0c2 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 110247de01764a544371d07eaed0308429a47daa
| author | iuc |
|---|---|
| date | Fri, 27 Oct 2017 19:40:36 -0400 |
| parents | 3bad335ccea9 |
| children | 39f063be9fb4 |
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| 0:3bad335ccea9 | 1:6999173dc0c2 |
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| 106 #end for | 106 #end for |
| 107 #elif str($repeat.software_cond.software) == "featureCounts" | 107 #elif str($repeat.software_cond.software) == "featureCounts" |
| 108 #for $file in $repeat.software_cond.input | 108 #for $file in $repeat.software_cond.input |
| 109 #set file_prefix = $software_dir + '/' + str($file.element_identifier) | 109 #set file_prefix = $software_dir + '/' + str($file.element_identifier) |
| 110 #if $file.metadata.column_names and $file.metadata.column_names.find(',') != -1 | 110 #if $file.metadata.column_names and $file.metadata.column_names.find(',') != -1 |
| 111 echo '$file.metadata.column_names.replace(',','\t').replace('__ob__u','').replace('u__sq__','').replace('__sq__','').replace('__cb__','')' >> '$file_prefix.summary' && | 111 echo '$file.metadata.column_names.replace(',','\t').replace('__ob__u','').replace('u__sq__','').replace('__sq__','').replace('__cb__','')' >> '${file_prefix}.summary' && |
| 112 cat '$file' >> '${file_prefix}.summary' && | 112 cat '$file' >> '${file_prefix}.summary' && |
| 113 #else | 113 #else |
| 114 ln -s '$file' '${file_prefix}.summary' && | 114 ln -s '$file' '${file_prefix}.summary' && |
| 115 #end if | 115 #end if |
| 116 #end for | 116 #end for |
| 320 #set $configfile = "T" | 320 #set $configfile = "T" |
| 321 #for $j, $file in enumerate( $repeat.software_cond.input ) | 321 #for $j, $file in enumerate( $repeat.software_cond.input ) |
| 322 ln -s '$file' '${software_dir}/file_${i}_${j}' && | 322 ln -s '$file' '${software_dir}/file_${i}_${j}' && |
| 323 more $file && | 323 more $file && |
| 324 #end for | 324 #end for |
| 325 #end if | 325 #end if |
| 326 #end for | 326 #end for |
| 327 | 327 |
| 328 multiqc multiqc_WDir | 328 multiqc multiqc_WDir |
| 329 | 329 |
| 330 #if $configfile == "T" | 330 #if $configfile == "T" |
| 529 <when value="junction_annotation"> | 529 <when value="junction_annotation"> |
| 530 <param name="input" type="data" format="txt,xls,tabular" multiple="true" label="RSeQC junction_annotation output" help="It should contain 'Partial Novel Splicing Junctions:'"/> | 530 <param name="input" type="data" format="txt,xls,tabular" multiple="true" label="RSeQC junction_annotation output" help="It should contain 'Partial Novel Splicing Junctions:'"/> |
| 531 </when> | 531 </when> |
| 532 <when value="junction_saturation"> | 532 <when value="junction_saturation"> |
| 533 <param name="input" type="data" format="txt" multiple="true" label="RSeQC junction_saturation output"/> | 533 <param name="input" type="data" format="txt" multiple="true" label="RSeQC junction_saturation output"/> |
| 534 </when> | 534 </when> |
| 535 <when value="read_distribution"> | 535 <when value="read_distribution"> |
| 536 <param name="input" type="data" format="txt,xls,tabular" multiple="true" label="RSeQC read_distribution output" help="It should contain 'Group Total_bases Tag_count Tags/Kb'"/> | 536 <param name="input" type="data" format="txt,xls,tabular" multiple="true" label="RSeQC read_distribution output" help="It should contain 'Group Total_bases Tag_count Tags/Kb'"/> |
| 537 </when> | 537 </when> |
| 538 <when value="read_duplication_pos"> | 538 <when value="read_duplication_pos"> |
| 539 <param name="input" type="data" format="csv,xls,tabular" multiple="true" label="RSeQC read_duplication_pos output"/> | 539 <param name="input" type="data" format="csv,xls,tabular" multiple="true" label="RSeQC read_duplication_pos output"/> |