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comparison abundance_estimates_to_matrix.xml @ 20:a009c96c5c18 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1d443e73d2eb888660bbbc7af198f5bcca9c1a70
author iuc
date Tue, 11 Apr 2023 19:52:45 +0000
parents 442e3696c634
children 400691c87530
comparison
equal deleted inserted replaced
19:bcc5f03f1900 20:a009c96c5c18
1 <tool id="trinity_abundance_estimates_to_matrix" name="Build expression matrix" version="@WRAPPER_VERSION@"> 1 <tool id="trinity_abundance_estimates_to_matrix" name="Build expression matrix" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
2 <description>for a de novo assembly of RNA-Seq data by Trinity</description> 2 <description>for a de novo assembly of RNA-Seq data by Trinity</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="bio_tools"/> 6 <expand macro="bio_tools"/>
7 <expand macro="requirements"> 7 <expand macro="requirements"/>
8 <requirement type="package" version="3.20.7">bioconductor-edger</requirement>
9 <requirement type="package" version="0.44.0">kallisto</requirement>
10 </expand>
11 <command detect_errors="aggressive"><![CDATA[ 8 <command detect_errors="aggressive"><![CDATA[
12 #import re 9 #import re
13 #for $entry in $samples: 10 #for $entry in $samples:
14 ln -f -s '${entry}' '${re.sub('[^\w\-_]', '_', entry.element_identifier)}' && 11 ln -f -s '${entry}' '${re.sub('[^\w\-_]', '_', entry.element_identifier)}' &&
15 #end for 12 #end for
47 && mv *.gene.UpperQuartile.EXPR.matrix '$norm_UQ_gene' 44 && mv *.gene.UpperQuartile.EXPR.matrix '$norm_UQ_gene'
48 #end if 45 #end if
49 #end if 46 #end if
50 ]]></command> 47 ]]></command>
51 <inputs> 48 <inputs>
52 <param name="samples" label="Abundance estimates" type="data" multiple="true" format="tabular" help="output(s) from 'Align reads and estimate abundance' tool" /> 49 <param name="samples" type="data" format="tabular" multiple="true" label="Abundance estimates" help="output(s) from 'Align reads and estimate abundance' tool" />
53 <param format="tabular" name="gene_trans_map" argument="--gene_trans_map" type="data" label="Gene to transcript correspondence ('gene(tab)transcript' lines)" optional="true" help="Only needed for gene level estimates" /> 50 <param argument="--gene_trans_map" type="data" format="tabular" optional="true" label="Gene to transcript correspondence ('gene(tab)transcript' lines)" help="Only needed for gene level estimates" />
54 <param type="select" name="est_method" argument="--est_method" label="Abundance estimation method"> 51 <param type="select" argument="--est_method" label="Abundance estimation method">
55 <option value="RSEM">RSEM</option> 52 <option value="RSEM">RSEM</option>
56 <option value="eXpress">eXpress</option> 53 <option value="eXpress">eXpress</option>
57 <option value="salmon">Salmon</option> 54 <option value="salmon">Salmon</option>
58 <option value="kallisto">Kallisto</option> 55 <option value="kallisto">Kallisto</option>
59 </param> 56 </param>
60 57
61 <section name="additional_params" title="Additional Options" expanded="False"> 58 <section name="additional_params" title="Additional Options" expanded="False">
62 <param type="select" name="cross_sample_norm" argument="--cross_sample_norm" label="Cross sample normalization"> 59 <param type="select" argument="--cross_sample_norm" label="Cross sample normalization">
63 <option value="TMM">TMM</option> 60 <option value="TMM">TMM</option>
64 <option value="UpperQuartile">UpperQuartile</option> 61 <option value="UpperQuartile">UpperQuartile</option>
65 <option value="none">None</option> 62 <option value="none">None</option>
66 </param> 63 </param>
67 </section> 64 </section>
68 </inputs> 65 </inputs>
69 <outputs> 66 <outputs>
70 <data format="tabular" name="trans_counts" label="${tool.name} on ${on_string}: estimated RNA-Seq fragment isoform counts (raw counts)"/> 67 <data format="tabular" name="trans_counts" label="${tool.name} on ${on_string}: estimated RNA-Seq fragment isoform counts (raw counts)"/>
71 <data format="tabular" name="TPM_no_norm" label="${tool.name} on ${on_string}: matrix of isoform TPM expression values (not cross-sample normalized)"/> 68 <data format="tabular" name="TPM_no_norm" label="${tool.name} on ${on_string}: Matrix of isoform TPM expression values (not cross-sample normalized)"/>
72 69
73 <data format="tabular" name="trans_counts_gene" label="${tool.name} on ${on_string}: estimated RNA-Seq fragment gene counts (raw counts)"> 70 <data format="tabular" name="trans_counts_gene" label="${tool.name} on ${on_string}: estimated RNA-Seq fragment gene counts (raw counts)">
74 <filter>gene_trans_map</filter> 71 <filter>gene_trans_map</filter>
75 </data> 72 </data>
76 <data format="tabular" name="TPM_no_norm_gene" label="${tool.name} on ${on_string}: matrix of gene TPM expression values (not cross-sample normalized)"> 73 <data format="tabular" name="TPM_no_norm_gene" label="${tool.name} on ${on_string}: Matrix of gene TPM expression values (not cross-sample normalized)">
77 <filter>gene_trans_map</filter> 74 <filter>gene_trans_map</filter>
78 </data> 75 </data>
79 76
80 <data format="tabular" name="norm_TMM" label="${tool.name} on ${on_string}: matrix of TMM-normalized expression values"> 77 <data format="tabular" name="norm_TMM" label="${tool.name} on ${on_string}: Matrix of TMM-normalized expression values">
81 <filter>additional_params['cross_sample_norm'] == "TMM"</filter> 78 <filter>additional_params['cross_sample_norm'] == "TMM"</filter>
82 </data> 79 </data>
83 <data format="tabular" name="norm_UQ" label="${tool.name} on ${on_string}: matrix of UpperQuartile-normalized expression values"> 80 <data format="tabular" name="norm_UQ" label="${tool.name} on ${on_string}: Matrix of UpperQuartile-normalized expression values">
84 <filter>additional_params['cross_sample_norm'] == "UpperQuartile"</filter> 81 <filter>additional_params['cross_sample_norm'] == "UpperQuartile"</filter>
85 </data> 82 </data>
86 83
87 <data format="tabular" name="norm_TMM_gene" label="${tool.name} on ${on_string}: matrix of TMM-normalized expression values"> 84 <data format="tabular" name="norm_TMM_gene" label="${tool.name} on ${on_string}: Matrix of TMM-normalized expression values (gene)">
88 <filter>additional_params['cross_sample_norm'] == "TMM" and gene_trans_map</filter> 85 <filter>additional_params['cross_sample_norm'] == "TMM" and gene_trans_map</filter>
89 </data> 86 </data>
90 <data format="tabular" name="norm_UQ_gene" label="${tool.name} on ${on_string}: matrix of UpperQuartile-normalized expression values"> 87 <data format="tabular" name="norm_UQ_gene" label="${tool.name} on ${on_string}: Matrix of UpperQuartile-normalized expression values (gene)">
91 <filter>additional_params['cross_sample_norm'] == "UpperQuartile" and gene_trans_map</filter> 88 <filter>additional_params['cross_sample_norm'] == "UpperQuartile" and gene_trans_map</filter>
92 </data> 89 </data>
93 </outputs> 90 </outputs>
94 <tests> 91 <tests>
95 <test> 92 <test>