Mercurial > repos > iuc > trinity_abundance_estimates_to_matrix
comparison abundance_estimates_to_matrix.xml @ 20:a009c96c5c18 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1d443e73d2eb888660bbbc7af198f5bcca9c1a70
author | iuc |
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date | Tue, 11 Apr 2023 19:52:45 +0000 |
parents | 442e3696c634 |
children | 400691c87530 |
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19:bcc5f03f1900 | 20:a009c96c5c18 |
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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> |