Mercurial > repos > iuc > trinity_samples_qccheck
comparison samples_qccheck.xml @ 19:1b1a25f93f80 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 19:49:25 +0000 |
parents | 50ba95fec4a2 |
children | 04bb8bb7c198 |
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18:3a4ac03d1266 | 19:1b1a25f93f80 |
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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[ |