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comparison deseq2.xml @ 22:e5c8afac22a7 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
author iuc
date Mon, 04 Feb 2019 16:45:12 -0500
parents a6fc9228e1a0
children 71bacea10eee
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21:a6fc9228e1a0 22:e5c8afac22a7
1 <tool id="deseq2" name="DESeq2" version="2.11.40.5"> 1 <tool id="deseq2" name="DESeq2" version="2.11.40.6">
2 <description>Determines differentially expressed features from count tables</description> 2 <description>Determines differentially expressed features from count tables</description>
3 <macros>
4 <import>deseq2_macros.xml</import>
5 </macros>
3 <requirements> 6 <requirements>
4 <requirement type="package" version="1.20.0">bioconductor-deseq2</requirement> 7 <requirement type="package" version="1.22.1">bioconductor-deseq2</requirement>
5 <!-- Optional dependency of tximport, needed to import kallisto results https://github.com/galaxyproject/usegalaxy-playbook/issues/161 --> 8 <!-- Optional dependency of tximport, needed to import kallisto results https://github.com/galaxyproject/usegalaxy-playbook/issues/161 -->
6 <requirement type="package" version="2.24.0">bioconductor-rhdf5</requirement> 9 <requirement type="package" version="2.26.2">bioconductor-rhdf5</requirement>
7 <requirement type="package" version="1.8.0">bioconductor-tximport</requirement> 10 <requirement type="package" version="1.10.0">bioconductor-tximport</requirement>
8 <requirement type="package" version="1.32.3">bioconductor-genomicfeatures</requirement> 11 <requirement type="package" version="1.34.1">bioconductor-genomicfeatures</requirement>
9 <requirement type="package" version="1.20.2">r-getopt</requirement> 12 <requirement type="package" version="1.20.2">r-getopt</requirement>
10 <requirement type="package" version="0.8.0">r-ggrepel</requirement> 13 <requirement type="package" version="0.8.0">r-ggrepel</requirement>
11 <requirement type="package" version="3.0.1">r-gplots</requirement> 14 <requirement type="package" version="3.0.1">r-gplots</requirement>
12 <requirement type="package" version="1.0.10">r-pheatmap</requirement> 15 <requirement type="package" version="1.0.10">r-pheatmap</requirement>
13 <requirement type="package" version="0.2.20">r-rjson</requirement> 16 <requirement type="package" version="0.2.20">r-rjson</requirement>
55 #if $normVST: 58 #if $normVST:
56 -v '$vst_out' 59 -v '$vst_out'
57 #end if 60 #end if
58 #set $filename_to_element_identifiers = {} 61 #set $filename_to_element_identifiers = {}
59 #set $temp_factor_names = list() 62 #set $temp_factor_names = list()
60 #for $factor in $rep_factorName: 63 #for $factor in $select_data.rep_factorName:
61 #set $temp_factor = list() 64 #set $temp_factor = list()
62 #for $level in $factor.rep_factorLevel: 65 #for $level in $factor.rep_factorLevel:
63 #set $count_files = list() 66 #set $count_files = list()
64 #for $file in $level.countsFile: 67 #if $select_data.how == 'group_tags':
65 $count_files.append(str($file)) 68 #for $group in $level.groups.value:
66 $filename_to_element_identifiers.__setitem__(os.path.basename(str($file)), $file.element_identifier) 69 #for $file in $select_data.countsFile.get_datasets_for_group($group):
67 #end for 70 $count_files.append(str($file))
71 $filename_to_element_identifiers.__setitem__(os.path.basename(str($file)), $file.element_identifier)
72 #end for
73 #end for
74 #else:
75 #for $file in $level.countsFile:
76 $count_files.append(str($file))
77 $filename_to_element_identifiers.__setitem__(os.path.basename(str($file)), $file.element_identifier)
78 #end for
79 #end if
68 $temp_factor.append( {str($level.factorLevel): $count_files} ) 80 $temp_factor.append( {str($level.factorLevel): $count_files} )
69 #end for 81 #end for
70 $temp_factor.reverse() 82 $temp_factor.reverse()
71 $temp_factor_names.append([str($factor.factorName), $temp_factor]) 83 $temp_factor_names.append([str($factor.factorName), $temp_factor])
72 #end for 84 #end for
104 #end if 116 #end if
105 117
106 #end if 118 #end if
107 ]]></command> 119 ]]></command>
108 <inputs> 120 <inputs>
109 <repeat name="rep_factorName" title="Factor" min="1"> 121 <conditional name="select_data">
110 <param name="factorName" type="text" value="FactorName" label="Specify a factor name, e.g. effects_drug_x or cancer_markers" 122 <param name="how" type="select">
111 help="Only letters, numbers and underscores will be retained in this field"> 123 <option value="datasets_per_level">Select datasets per level</option>
112 <sanitizer> 124 <option value="group_tags">Select group tags corresponding to levels</option>
113 <valid initial="string.letters,string.digits"><add value="_" /></valid>
114 </sanitizer>
115 </param> 125 </param>
116 <repeat name="rep_factorLevel" title="Factor level" min="2" default="2"> 126 <when value="group_tags">
117 <param name="factorLevel" type="text" value="FactorLevel" label="Specify a factor level, typical values could be 'tumor', 'normal', 'treated' or 'control'" 127 <param name="countsFile" type="data_collection" format="tabular" label="Count file(s) collection" multiple="true"/>
118 help="Only letters, numbers and underscores will be retained in this field"> 128 <expand macro="factor_repeat">
119 <sanitizer> 129 <param name="groups" type="group_tag" data_ref="countsFile" multiple="true" label="Select groups that correspond to this factor level"/>
120 <valid initial="string.letters,string.digits"><add value="_" /></valid> 130 </expand>
121 </sanitizer> 131 </when>
122 </param> 132 <when value="datasets_per_level">
123 <param name="countsFile" type="data" format="tabular" multiple="true" label="Counts file(s)"/> 133 <expand macro="factor_repeat">
124 </repeat> 134 <param name="countsFile" type="data" format="tabular" multiple="true" label="Counts file(s)"/>
125 </repeat> 135 </expand>
136 </when>
137 </conditional>
138
126 <param name="batch_factors" type="data" format="tabular" optional="true" label="(Optional) provide a tabular file with additional batch factors to include in the model." help="You can produce this file using RUVSeq or svaseq."/> 139 <param name="batch_factors" type="data" format="tabular" optional="true" label="(Optional) provide a tabular file with additional batch factors to include in the model." help="You can produce this file using RUVSeq or svaseq."/>
127 <param name="header" type="boolean" truevalue="-H" falsevalue="" checked="true" label="Files have header?" help="If this option is set to Yes, the tool will assume that the count files have column headers in the first row. Default: Yes" /> 140 <param name="header" type="boolean" truevalue="-H" falsevalue="" checked="true" label="Files have header?" help="If this option is set to Yes, the tool will assume that the count files have column headers in the first row. Default: Yes" />
128 141
129 <conditional name="tximport"> 142 <conditional name="tximport">
130 <param name="tximport_selector" type="select" label="Choice of Input data"> 143 <param name="tximport_selector" type="select" label="Choice of Input data">
395 <assert_contents> 408 <assert_contents>
396 <has_text_matching expression="ENSG00000168671\t1.8841.*\t-0.1180.*\t0.7429.*\t-0.1589.*\t0.8737.*\t0.9999.*" /> 409 <has_text_matching expression="ENSG00000168671\t1.8841.*\t-0.1180.*\t0.7429.*\t-0.1589.*\t0.8737.*\t0.9999.*" />
397 </assert_contents> 410 </assert_contents>
398 </output> 411 </output>
399 </test> 412 </test>
413 <!--Ensure group tags can be used to select factor levels -->
414 <test expect_num_outputs="1">
415 <param name="select_data|how" value="group_tags"/>
416 <param name="select_data|countsFile">
417 <collection type="list">
418 <element name="1" value="sailfish/sailfish_quant.sf1.tab" tags="group:primary:treated"/>
419 <element name="2" value="sailfish/sailfish_quant.sf2.tab" tags="group:primary:treated"/>
420 <element name="3" value="sailfish/sailfish_quant.sf3.tab" tags="group:primary:treated"/>
421 <element name="4" value="sailfish/sailfish_quant.sf4.tab" tags="group:primary:untreated"/>
422 <element name="5" value="sailfish/sailfish_quant.sf5.tab" tags="group:primary:untreated"/>
423 <element name="6" value="sailfish/sailfish_quant.sf6.tab" tags="group:primary:untreated"/>
424 </collection>
425 </param>
426 <repeat name="rep_factorName">
427 <param name="factorName" value="Treatment"/>
428 <repeat name="rep_factorLevel">
429 <param name="factorLevel" value="Treated"/>
430 <param name="groups" value="primary:treated"/>
431 </repeat>
432 <repeat name="rep_factorLevel">
433 <param name="factorLevel" value="Untreated"/>
434 <param name="groups" value="primary:untreated"/>
435 </repeat>
436 </repeat>
437 <param name="pdf" value="False"/>
438 <param name="tximport_selector" value="tximport"/>
439 <param name="txtype" value="sailfish"/>
440 <param name="mapping_format_selector" value="tabular"/>
441 <param name="tabular_file" value="tx2gene.tab"/>
442 <output name="deseq_out" >
443 <assert_contents>
444 <has_text_matching expression="HOXC11\t0.557.*\t0.324.*\t0.437.*\t0.741.*\t0.458.*\t0.999.*"/>
445 </assert_contents>
446 </output>
447 </test>
400 </tests> 448 </tests>
401 <help><![CDATA[ 449 <help><![CDATA[
402 .. class:: infomark 450 .. class:: infomark
403 451
404 **What it does** 452 **What it does**