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comparison multiqc.xml @ 1:6999173dc0c2 draft

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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
comparison
equal deleted inserted replaced
0:3bad335ccea9 1:6999173dc0c2
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"/>