Mercurial > repos > iuc > trinity_samples_qccheck

comparison samples_qccheck.xml @ 19:3255ea2cae66 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 19:38:25 +0000
parents 7f5fc85ff6ae
children 92eb9747c391
comparison
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18:cb491be4155f 19:3255ea2cae66
1 <tool id="trinity_samples_qccheck" name="RNASeq samples quality check" version="@WRAPPER_VERSION@"> 1 <tool id="trinity_samples_qccheck" name="RNASeq samples quality check" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
2 <description>for transcript quantification</description> 2 <description>for transcript quantification</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="2.38.0">bioconductor-biobase</requirement>
9 <requirement type="package" version="2.10.0">bioconductor-qvalue</requirement>
10 <requirement type="package" version="2.0.6">r-cluster</requirement>
11 <requirement type="package" version="1.1.24">r-fastcluster</requirement>
12 </expand>
13 <command detect_errors="aggressive"><![CDATA[ 8 <command detect_errors="aggressive"><![CDATA[
14 9
15 ln -f -s '${matrix}' "input.matrix" 10 ln -f -s '${matrix}' input.matrix
16
17 && 11 &&
18
19 PtR 12 PtR
20 --matrix "input.matrix" 13 --matrix input.matrix
21
22 --samples '${samples}' 14 --samples '${samples}'
23
24 --CPM --log2 --compare_replicates 15 --CPM --log2 --compare_replicates
25
26 && 16 &&
27
28 PtR 17 PtR
29 --matrix "input.matrix" 18 --matrix input.matrix
30
31 --samples '${samples}' 19 --samples '${samples}'
32
33 --CPM --log2 --sample_cor_matrix 20 --CPM --log2 --sample_cor_matrix
34
35 && 21 &&
36
37 PtR 22 PtR
38 --matrix "input.matrix" 23 --matrix input.matrix
39
40 --samples '${samples}' 24 --samples '${samples}'
41 25 --CPM --log2
42 --CPM --log2 --prin_comp 3 26 --prin_comp 3
43
44 && mkdir out_pdf 27 && mkdir out_pdf
45 && mv *rep_compare.pdf out_pdf/ 28 && mv *rep_compare.pdf out_pdf/
46 && mv *sample_cor_matrix.pdf out_pdf/ 29 && mv *sample_cor_matrix.pdf out_pdf/
47 && mv *principal_components.pdf out_pdf/ 30 && mv *principal_components.pdf out_pdf/
48 31
49 ]]></command> 32 ]]></command>
50 <inputs> 33 <inputs>
51 <param format="tabular" name="matrix" argument="--matrix" type="data" label="Expression matrix" help="output of abundance_estimates_to_matrix tool"/> 34 <param argument="--matrix" format="tabular" type="data" label="Expression matrix" help="Output of abundance_estimates_to_matrix tool"/>
52 <param format="tabular" name="samples" argument="--samples" type="data" label="Samples description" help="file describing samples and replicates"/> 35 <param argument="--samples" format="tabular" type="data" label="Samples description" help="File describing samples and replicates"/>
53 </inputs> 36 </inputs>
54 <outputs> 37 <outputs>
55 <collection name="reports" type="list" label="Quality check result files on ${on_string}"> 38 <collection name="reports" type="list" label="Quality check result files on ${on_string}">
56 <discover_datasets pattern="__name__" ext="pdf" directory="out_pdf" /> 39 <discover_datasets pattern="__name__" ext="pdf" directory="out_pdf" />
57 </collection> 40 </collection>
58 </outputs> 41 </outputs>
59 <tests> 42 <tests>
60 <test> 43 <test>
61 <param name="matrix" value="count/qcheck/matrix.counts.matrix"/> 44 <param name="matrix" value="count/qcheck/matrix.counts.matrix" ftype="tabular" />
62 <param name="samples" value="count/samples.txt"/> 45 <param name="samples" value="count/samples.txt" ftype="tabular"/>
63 <output_collection name="reports"> 46 <output_collection name="reports">
47 <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"/>
48 <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"/>
64 <element name="wt_37.rep_compare.pdf" compare="sim_size" delta="100" file="count/qcheck/wt_37.rep_compare.pdf"/> 49 <element name="wt_37.rep_compare.pdf" compare="sim_size" delta="100" file="count/qcheck/wt_37.rep_compare.pdf"/>
65 <element name="wt_GSNO.rep_compare.pdf" compare="sim_size" delta="100" file="count/qcheck/wt_GSNO.rep_compare.pdf"/> 50 <element name="wt_GSNO.rep_compare.pdf" compare="sim_size" delta="100" file="count/qcheck/wt_GSNO.rep_compare.pdf"/>
66 <element name="wt_ph8.rep_compare.pdf" compare="sim_size" delta="100" file="count/qcheck/wt_ph8.rep_compare.pdf"/> 51 <element name="wt_ph8.rep_compare.pdf" compare="sim_size" delta="100" file="count/qcheck/wt_ph8.rep_compare.pdf"/>
67 <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"/>
68 <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"/>
69 </output_collection> 52 </output_collection>
70 </test> 53 </test>
71 </tests> 54 </tests>
72 <help> 55 <help>
73 <![CDATA[ 56 <![CDATA[