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