annotate rankprod2.xml @ 5:b2b5f193f5bd draft

Uploaded
author enios
date Wed, 21 Apr 2021 10:54:52 +0000
parents e3546c89d20e
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
3
e3546c89d20e Uploaded
enios
parents:
diff changeset
1 <tool id="rankprodthree" name="RankProd" >
e3546c89d20e Uploaded
enios
parents:
diff changeset
2 <requirements>
e3546c89d20e Uploaded
enios
parents:
diff changeset
3 <container type="docker">bianca7/lncrna:rankprod</container>
e3546c89d20e Uploaded
enios
parents:
diff changeset
4 </requirements>
e3546c89d20e Uploaded
enios
parents:
diff changeset
5 <description>Differential expression with RankProd</description>
e3546c89d20e Uploaded
enios
parents:
diff changeset
6 <stdio>
e3546c89d20e Uploaded
enios
parents:
diff changeset
7 <exit_code range="1:" level="fatal" />
e3546c89d20e Uploaded
enios
parents:
diff changeset
8 </stdio>
e3546c89d20e Uploaded
enios
parents:
diff changeset
9 <command><![CDATA[
e3546c89d20e Uploaded
enios
parents:
diff changeset
10 #if $choose.genes=='T'
e3546c89d20e Uploaded
enios
parents:
diff changeset
11 Rscript /logrankprod.R "c($whichcols)" $file1 "c($whichrows)" $sc $file2 $file3 $norm $base $log $choose.genes $choose.numgenes
e3546c89d20e Uploaded
enios
parents:
diff changeset
12 #end if
e3546c89d20e Uploaded
enios
parents:
diff changeset
13 #if $choose.genes=='F'
e3546c89d20e Uploaded
enios
parents:
diff changeset
14 Rscript /logrankprod.R "c($whichcols)" $file1 "c($whichrows)" $sc $file2 $file3 $norm $base $log $choose.genes $choose.method $choose.cutoff
e3546c89d20e Uploaded
enios
parents:
diff changeset
15 #end if
e3546c89d20e Uploaded
enios
parents:
diff changeset
16 ]]></command>
e3546c89d20e Uploaded
enios
parents:
diff changeset
17 <inputs>
e3546c89d20e Uploaded
enios
parents:
diff changeset
18 <param format="tabular, txt" name="file1" type="data" label="input matrix" />
e3546c89d20e Uploaded
enios
parents:
diff changeset
19 <param name="whichcols" type="text" label="Comma separated fields for columns, like 1,2,3,4" />
e3546c89d20e Uploaded
enios
parents:
diff changeset
20 <param name="sc" type="integer" value="1" label="Choose col class" />
e3546c89d20e Uploaded
enios
parents:
diff changeset
21 <param format="tabular, txt" name="file2" type="data" label="input samples matrix" />
e3546c89d20e Uploaded
enios
parents:
diff changeset
22 <param name="whichrows" type="text" label="Comma separated fields for rows" />
e3546c89d20e Uploaded
enios
parents:
diff changeset
23 <param name="norm" type="boolean" truevalue="T" falsevalue="F" selected="FALSE" label="Are counts normalized?" />
e3546c89d20e Uploaded
enios
parents:
diff changeset
24 <param name="base" type="select" label="Choose log base" >
e3546c89d20e Uploaded
enios
parents:
diff changeset
25 <option value="2">2</option>
e3546c89d20e Uploaded
enios
parents:
diff changeset
26 <option value="10">10</option>
e3546c89d20e Uploaded
enios
parents:
diff changeset
27 </param>
e3546c89d20e Uploaded
enios
parents:
diff changeset
28 <param name="log" type="boolean" truevalue="T" falsevalue="F" selected="FALSE" label="Are they logarithmically transformed?" />
e3546c89d20e Uploaded
enios
parents:
diff changeset
29 <conditional name="choose" >
e3546c89d20e Uploaded
enios
parents:
diff changeset
30 <param name="genes" type="boolean" truevalue="T" falsevalue="F" checked="no" label="Select specific genes or choose method" />
e3546c89d20e Uploaded
enios
parents:
diff changeset
31 <when value="T">
e3546c89d20e Uploaded
enios
parents:
diff changeset
32 <param name="numgenes" type="integer" value="10" label="How many genes" />
e3546c89d20e Uploaded
enios
parents:
diff changeset
33 </when>
e3546c89d20e Uploaded
enios
parents:
diff changeset
34 <when value="F">
e3546c89d20e Uploaded
enios
parents:
diff changeset
35 <param name="method" type="select" label="Select method" >
e3546c89d20e Uploaded
enios
parents:
diff changeset
36 <option value="pfp">pfp</option>
e3546c89d20e Uploaded
enios
parents:
diff changeset
37 <option value="pval">pval</option>
e3546c89d20e Uploaded
enios
parents:
diff changeset
38 </param>
e3546c89d20e Uploaded
enios
parents:
diff changeset
39 <param name="cutoff" type="float" value="0.05" label="Choose cutoff" />
e3546c89d20e Uploaded
enios
parents:
diff changeset
40 </when>
e3546c89d20e Uploaded
enios
parents:
diff changeset
41 </conditional>
e3546c89d20e Uploaded
enios
parents:
diff changeset
42 </inputs>
e3546c89d20e Uploaded
enios
parents:
diff changeset
43 <outputs>
e3546c89d20e Uploaded
enios
parents:
diff changeset
44 <data format="txt" name="file3" label="Differentially expressed molecules"/>
e3546c89d20e Uploaded
enios
parents:
diff changeset
45 </outputs>
e3546c89d20e Uploaded
enios
parents:
diff changeset
46 </tool>