Mercurial > repos > vijay > pancancer_compare_within_models

annotate compare_within_models.xml @ 0:84ac2a86bde1 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 23:29:26 +0000
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84ac2a86bde1 "planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
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1 <tool id="pancancer_compare_within_models" name="PAPAA: PanCancer compare within models" version="@VERSION@">
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2 <description>compare within models</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_compare_within_models.R' --version 2>&1 | grep PAPAA]]></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 '${pancan_classifier_summary}' 'classifier/classifier_summary.txt' &&
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13 ln -s '${pancan_classifier_coefficients}' 'classifier/classifier_coefficients.tsv' &&
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14 #for $within_summary in $pancan_within_classifier_summary:
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15 mkdir -p 'classifier/within_disease/${within_summary.element_identifier}' &&
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16 ln -s '${within_summary}' 'classifier/within_disease/${within_summary.element_identifier}/classifier_summary.txt' &&
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17 #end for
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18 #for $within_coefficient in $pancan_within_classifier_coefficients:
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19 mkdir -p 'classifier/within_disease/${within_coefficient.element_identifier}' &&
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20 ln -s '${within_coefficient}' 'classifier/within_disease/${within_coefficient.element_identifier}/classifier_coefficients.tsv' &&
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21 #end for
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22 #if $include_alt.include_alt_select == 'true':
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23 mkdir 'alt_classifier' &&
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24 ln -s '${include_alt.alt_pancan_classifier_summary}' 'alt_classifier/classifier_summary.txt' &&
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25 ln -s '${include_alt.alt_pancan_classifier_coefficients}' 'alt_classifier/classifier_coefficients.tsv' &&
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26 #for $within_summary in $include_alt.alt_pancan_within_classifier_summary:
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27 mkdir -p 'alt_classifier/within_disease/${within_summary.element_identifier}' &&
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28 ln -s '${within_summary}' 'alt_classifier/within_disease/${within_summary.element_identifier}/classifier_summary.txt' &&
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29 #end for
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30 #for $within_coefficient in $include_alt.alt_pancan_within_classifier_coefficients:
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31 mkdir -p 'alt_classifier/within_disease/${within_coefficient.element_identifier}' &&
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32 ln -s '${within_coefficient}' 'alt_classifier/within_disease/${within_coefficient.element_identifier}/classifier_coefficients.tsv' &&
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33 #end for
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34 #end if
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35 ls -lahR &&
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36 papaa_compare_within_models.R
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37 --pancan_model 'classifier'
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38 #if $include_alt.include_alt_select == 'true':
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39 --alt_model 'alt_classifier'
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40 #end if
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41 > '${log}'
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42 ]]>
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43 </command>
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44 <inputs>
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45 <param argument="--pancan_model" label="pancancer classifier summary" name="pancan_classifier_summary" optional="false" type="data" format="txt" help="classifer_summary.txt"/>
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46 <param label="pancancer classifier coefficients" name="pancan_classifier_coefficients" optional="false" type="data" format="tabular" help="classifier_coefficients.tsv"/>
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47 <param label="pan_within classifier summary" name="pancan_within_classifier_summary" optional="false" type="data" format="txt" multiple="true" help="multiple classifer_summary.txt"/>
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48 <param label="pan_within classifier coefficients" name="pancan_within_classifier_coefficients" optional="false" type="data" format="tabular" multiple="true" help="multiple classifier_coefficients.tsv"/>
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49 <conditional name="include_alt">
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50 <param name="include_alt_select" type="select" label="Would you want to compare given model with alt gene model?" help="output of pancancer classifier and pancancer within disease for alt gene">
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51 <option value="false" selected="true">do not do alt gene</option>
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52 <option value="true">do alt gene</option>
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53 </param>
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54 <when value="true">
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55 <param argument="--alt_model" label="pancancer classifier summary" name="alt_pancan_classifier_summary" optional="false" type="data" format="txt" help="alt classifer_summary.txt"/>
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56 <param label="pancancer classifier coefficients" name="alt_pancan_classifier_coefficients" optional="false" type="data" format="tabular" help="alt classifier_coefficients.tsv"/>
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57 <param argument="pan_within classifier summary" label="alt_pancan_within_classifier_summary" name="alt_pancan_within_classifier_summary" optional="true" type="data" format="txt" multiple="true" help="multiple alt classifer_summary.txt"/>
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58 <param label="alt_pancan_within classifier coefficients" name="alt_pancan_within_classifier_coefficients" optional="true" type="data" format="tabular" multiple="true" help="multiple alt classifier_coefficients.tsv"/>
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59 </when>
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60 <when value="false">
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61 </when>
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62 </conditional>
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63 </inputs>
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64 <outputs>
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65 <data format="txt" name="log" label="${tool.name} on ${on_string} (Log)" />
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66 <data format="pdf" name="aupr_comparison" label="${tool.name} on ${on_string} (aupr_comparison.pdf)" from_work_dir="classifier/figures/aupr_comparison.pdf"/>
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67 <data format="pdf" name="auroc_comparison" label="${tool.name} on ${on_string} (auroc_comparison.pdf)" from_work_dir="classifier/figures/auroc_comparison.pdf"/>
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68 <data format="pdf" name="alt_gene_aupr_comparison" label="${tool.name} on ${on_string} (alt_gene_aupr_comparison.pdf)" from_work_dir="classifier/figures/alt_gene_aupr_comparison.pdf" >
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69 <filter>include_alt['include_alt_select'] == 'true' </filter>
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70 </data>
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71 <data format="pdf" name="alt_gene_auroc_comparison" label="${tool.name} on ${on_string} (alt_gene_auroc_comparison.pdf)" from_work_dir="classifier/figures/alt_gene_auroc_comparison.pdf" >
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72 <filter>include_alt['include_alt_select'] == 'true' </filter>
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73 </data>
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74 </outputs>
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75 <tests>
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76 <test>
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77 <param name="pancan_classifier_summary" value="classifier_summary.txt" ftype="txt"/>
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78 <param name="pancan_classifier_coefficients" value="classifier_coefficients.tsv" ftype="tabular"/>
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79 <param name="pancan_within_classifier_summary" value="classifier_summary/GBM" > <!--
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80 <collection type="list">
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81 <element name="GBM" value="GBM_100.txt" ftype="txt"/>
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82 </collection> -->
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83 </param>
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84 <param name="pancan_within_classifier_coefficients" value="classifier_coefficients/GBM"> <!--
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85 <collection type="list">
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86 <element name="GBM" value="GBM_99.tabular" ftype="tabular"/>
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87 </collection> -->
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88 </param>
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89 <param name="include_alt_select" value="false"/>
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90 <!--
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91 <conditional name="include_alt">
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92 <param name="include_alt_select" value="false"/>
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93 <param name="alt_pancan_summary" value="alt_pancan_summary.txt" ftype="txt"/>
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94 <param name="alt_pancan_classifier_coefficients" value="alt_pancan_classifier_coefficients.tsv" ftype="tabular"/>
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95 <param name="alt_pan_within_classifier_summary" value="alt_pan_within_classifier_summary.txt" ftype="txt"/>
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96 <param name="alt_pan_within_classifier_coefficients" value="alt_pan_within_classifier_coefficients.tsv" ftype="tabular"/>
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97 </conditional>
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98 -->
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99 <output name="log" file="compare_within_models_Log.txt"/>
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100 <output name="aupr_comparison" file="aupr_comparison.pdf" compare="sim_size" delta="50"/>
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101 <output name="auroc_comparison" file="auroc_comparison.pdf" compare="sim_size" delta="50"/>
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102
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103 </test>
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104 </tests>
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105 <help><![CDATA[
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106
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107 **Pancancer_Aberrant_Pathway_Activity_Analysis scripts/papaa_compare_within_models.R:**
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108
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109 **Inputs:**
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110 --pancan_model String of the Directory: location of Pan classifier summary file
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111 --alt_model String of the Directory: location of Alt gene classifier summary file
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112
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113 **Outputs:**
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114 Comparison plots for Pan and Pan_within models ("auroc_comparison.pdf" and "aupr_comparison.pdf")
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115
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116 Comparison plots for altgene, alt_within, Pan_alt models ("alt_gene_auroc_comparison.pdf" and "alt_gene_aupr_comparison.pdf") ]]>
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117
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118 </help>
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119 <expand macro="citations" />
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120 </tool>