Mercurial > repos > vijay > pancancer_external_sample_status_prediction

comparison external_sample_status_prediction.xml @ 0:8f426aeccfe3 draft default tip

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"planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
author vijay
date Wed, 16 Dec 2020 23:30:03 +0000
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-1:000000000000 0:8f426aeccfe3
1 <tool id="pancancer_external_sample_status_prediction" name="PAPAA: PanCancer external sample status prediction" version="@VERSION@">
2 <description>external sample status</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <expand macro="stdio"/>
8 <version_command><![CDATA['papaa_external_sample_pred_targene_classifier.py' --version]]></version_command>
9 <command><![CDATA[
10 mkdir 'classifier' &&
11 mkdir -p 'classifier/figures' &&
12 ln -s '${classifier_summary}' 'classifier/classifier_summary.txt' &&
13 ln -s '${pancan_classifier_coefficients}' 'classifier/classifier_coefficients.tsv' &&
14 papaa_external_sample_pred_targene_classifier.py
15 --classifier_summary 'classifier'
16 #if $ex_vlog and str($ex_vlog):
17 --expression_file '$ex_vlog'
18 #end if
19 #if $sign and str($sign):
20 --status_sign '$sign'
21 #end if
22 --figure1 '${figure1}'
23 --figure2 '${figure2}'
24 > '${log}'
25 ]]>
26 </command>
27 <inputs>
28 <param argument="--classifier_summary" label="Classifier data" name="classifier_summary" optional="false" type="data" format="txt" help="classifer_summary.txt"/>
29 <param label="pancancer classifier coefficients" name="pancan_classifier_coefficients" optional="false" type="data" format="tabular" help="classifier_coefficients.tsv"/>
30 <param argument="--expression_file" label="external sample gene expression data" name="ex_vlog" optional="false" type="data" format="csv" help="data/vlog_trans.csv" />
31 <param argument="--status_sign" label="given mutational status" name="sign" optional="false" type="data" format="txt" help="data/sign.txt" />
32 </inputs>
33 <outputs>
34 <data format="txt" name="log" label="${tool.name} on ${on_string} (Log)" />
35 <data format="pdf" name="figure1" label="${tool.name} on ${on_string} (Figure 1)" />
36 <data format="pdf" name="figure2" label="${tool.name} on ${on_string} (Figure 2)" />
37 </outputs>
38 <tests>
39 <test>
40 <param name="classifier_summary" value="classifier_summary.txt" ftype="txt"/>
41 <param name="pancan_classifier_coefficients" value="classifier_coefficients.tsv" ftype="tabular"/>
42 <param name="ex_vlog" value="vlog_trans.csv.gz" ftype="csv"/>
43 <param name="sign" value="sign.txt" ftype="txt"/>
44 <output name="log" file="external_sample_status_prediction_Log.txt" />
45 <output name="figure1" file="Figure_1.pdf" compare="sim_size" delta="50"/>
46 <output name="figure2" file="Figure_2.pdf" compare="sim_size" delta="50"/>
47 </test>
48 </tests>
49 <help><![CDATA[
50
51 **Pancancer_Aberrant_Pathway_Activity_Analysis scripts/papaa_external_sample_pred_targene_classifier.py:**
52
53 **Inputs:**
54 --classifier_summary String of the location of classifier scores file
55
56 --expression_file File path for external sample expression data file (fpkm/rpkm/rlog/vlog/nlog values)
57
58 --status_sign Provide sign for tumor/mutant [1] or normal/WT [-1] along with sorted sample names
59
60 **Outputs:**
61 Model based classification scores distribution Plots for external normal and tumor samples ("targene_external_sample_predictions.pdf and targene_external_sample_predictions_1.pdf") ]]>
62
63 </help>
64 <expand macro="citations" />
65 </tool>