Mercurial > repos > iuc > trinity_samples_qccheck
diff samples_qccheck.xml @ 19:1b1a25f93f80 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1d443e73d2eb888660bbbc7af198f5bcca9c1a70
| author | iuc |
|---|---|
| date | Tue, 11 Apr 2023 19:49:25 +0000 |
| parents | 50ba95fec4a2 |
| children | 04bb8bb7c198 |
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--- a/samples_qccheck.xml Sun Dec 19 16:19:58 2021 +0000 +++ b/samples_qccheck.xml Tue Apr 11 19:49:25 2023 +0000 @@ -1,46 +1,29 @@ -<tool id="trinity_samples_qccheck" name="RNASeq samples quality check" version="@WRAPPER_VERSION@"> +<tool id="trinity_samples_qccheck" name="RNASeq samples quality check" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> <description>for transcript quantification</description> <macros> <import>macros.xml</import> </macros> <expand macro="bio_tools"/> - <expand macro="requirements"> - <requirement type="package" version="2.38.0">bioconductor-biobase</requirement> - <requirement type="package" version="2.10.0">bioconductor-qvalue</requirement> - <requirement type="package" version="2.0.6">r-cluster</requirement> - <requirement type="package" version="1.1.24">r-fastcluster</requirement> - </expand> + <expand macro="requirements"/> <command detect_errors="aggressive"><![CDATA[ - ln -f -s '${matrix}' "input.matrix" - + ln -f -s '${matrix}' input.matrix && - PtR - --matrix "input.matrix" - + --matrix input.matrix --samples '${samples}' - --CPM --log2 --compare_replicates - && - PtR - --matrix "input.matrix" - + --matrix input.matrix --samples '${samples}' - --CPM --log2 --sample_cor_matrix - && - PtR - --matrix "input.matrix" - + --matrix input.matrix --samples '${samples}' - - --CPM --log2 --prin_comp 3 - + --CPM --log2 + --prin_comp 3 && mkdir out_pdf && mv *rep_compare.pdf out_pdf/ && mv *sample_cor_matrix.pdf out_pdf/ @@ -48,8 +31,8 @@ ]]></command> <inputs> - <param format="tabular" name="matrix" argument="--matrix" type="data" label="Expression matrix" help="output of abundance_estimates_to_matrix tool"/> - <param format="tabular" name="samples" argument="--samples" type="data" label="Samples description" help="file describing samples and replicates"/> + <param argument="--matrix" format="tabular" type="data" label="Expression matrix" help="Output of abundance_estimates_to_matrix tool"/> + <param argument="--samples" format="tabular" type="data" label="Samples description" help="File describing samples and replicates"/> </inputs> <outputs> <collection name="reports" type="list" label="Quality check result files on ${on_string}"> @@ -58,14 +41,14 @@ </outputs> <tests> <test> - <param name="matrix" value="count/qcheck/matrix.counts.matrix"/> - <param name="samples" value="count/samples.txt"/> + <param name="matrix" value="count/qcheck/matrix.counts.matrix" ftype="tabular" /> + <param name="samples" value="count/samples.txt" ftype="tabular"/> <output_collection name="reports"> + <element name="input.matrix.CPM.log2.prcomp.principal_components.pdf" compare="sim_size" delta="100" file="count/qcheck/input.matrix.CPM.log2.prcomp.principal_components.pdf"/> + <element name="input.matrix.CPM.log2.sample_cor_matrix.pdf" compare="sim_size" delta="100" file="count/qcheck/input.matrix.CPM.log2.sample_cor_matrix.pdf"/> <element name="wt_37.rep_compare.pdf" compare="sim_size" delta="100" file="count/qcheck/wt_37.rep_compare.pdf"/> <element name="wt_GSNO.rep_compare.pdf" compare="sim_size" delta="100" file="count/qcheck/wt_GSNO.rep_compare.pdf"/> <element name="wt_ph8.rep_compare.pdf" compare="sim_size" delta="100" file="count/qcheck/wt_ph8.rep_compare.pdf"/> - <element name="input.matrix.CPM.log2.prcomp.principal_components.pdf" compare="sim_size" delta="100" file="count/qcheck/input.matrix.CPM.log2.prcomp.principal_components.pdf"/> - <element name="input.matrix.CPM.log2.sample_cor_matrix.pdf" compare="sim_size" delta="100" file="count/qcheck/input.matrix.CPM.log2.sample_cor_matrix.pdf"/> </output_collection> </test> </tests>