Mercurial > repos > iuc > trinity_samples_qccheck

comparison samples_qccheck.xml @ 9:226663afe49c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
author iuc
date Thu, 14 Jun 2018 03:13:56 -0400
parents 8bec0d476fa0
children b58468eb4e64
comparison
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8:1812dbc5bb7b 9:226663afe49c
1 <tool id="trinity_samples_qccheck" name="RNASeq samples quality check" version="@WRAPPER_VERSION@.0"> 1 <tool id="trinity_samples_qccheck" name="RNASeq samples quality check" version="@WRAPPER_VERSION@">
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="requirements"> 6 <expand macro="requirements">
7 <requirement type="package" version="2.34.0">bioconductor-biobase</requirement> 7 <requirement type="package" version="2.38.0">bioconductor-biobase</requirement>
8 <requirement type="package" version="2.6.0">bioconductor-qvalue</requirement> 8 <requirement type="package" version="2.10.0">bioconductor-qvalue</requirement>
9 <requirement type="package" version="2.0.6">r-cluster</requirement> 9 <requirement type="package" version="2.0.6">r-cluster</requirement>
10 <requirement type="package" version="1.1.24">r-fastcluster</requirement>
10 </expand> 11 </expand>
11 <command detect_errors="aggressive"><![CDATA[ 12 <command detect_errors="aggressive"><![CDATA[
12 13
13 ln -f -s "${matrix}" "input.matrix" 14 ln -f -s '${matrix}' "input.matrix"
14 15
15 && 16 &&
16 17
17 PtR 18 PtR
18 --matrix "input.matrix" 19 --matrix "input.matrix"
19 20
20 --samples "${samples}" 21 --samples '${samples}'
21 22
22 --CPM --log2 --compare_replicates 23 --CPM --log2 --compare_replicates
23 24
24 && 25 &&
25 26
26 PtR 27 PtR
27 --matrix "input.matrix" 28 --matrix "input.matrix"
28 29
29 --samples "${samples}" 30 --samples '${samples}'
30 31
31 --CPM --log2 --sample_cor_matrix 32 --CPM --log2 --sample_cor_matrix
32 33
33 && 34 &&
34 35
35 PtR 36 PtR
36 --matrix "input.matrix" 37 --matrix "input.matrix"
37 38
38 --samples "${samples}" 39 --samples '${samples}'
39 40
40 --CPM --log2 --prin_comp 3 41 --CPM --log2 --prin_comp 3
41 42
42 && mkdir out_pdf 43 && mkdir out_pdf
43 && mv *rep_compare.pdf out_pdf/ 44 && mv *rep_compare.pdf out_pdf/
60 <param name="samples" value="count/samples.txt"/> 61 <param name="samples" value="count/samples.txt"/>
61 <output_collection name="reports"> 62 <output_collection name="reports">
62 <element name="wt_37.rep_compare.pdf" compare="sim_size" delta="100" file="count/qcheck/wt_37.rep_compare.pdf"/> 63 <element name="wt_37.rep_compare.pdf" compare="sim_size" delta="100" file="count/qcheck/wt_37.rep_compare.pdf"/>
63 <element name="wt_GSNO.rep_compare.pdf" compare="sim_size" delta="100" file="count/qcheck/wt_GSNO.rep_compare.pdf"/> 64 <element name="wt_GSNO.rep_compare.pdf" compare="sim_size" delta="100" file="count/qcheck/wt_GSNO.rep_compare.pdf"/>
64 <element name="wt_ph8.rep_compare.pdf" compare="sim_size" delta="100" file="count/qcheck/wt_ph8.rep_compare.pdf"/> 65 <element name="wt_ph8.rep_compare.pdf" compare="sim_size" delta="100" file="count/qcheck/wt_ph8.rep_compare.pdf"/>
65 <element name="input.matrix.CPM.log2.principal_components.pdf" compare="sim_size" delta="100" file="count/qcheck/input.matrix.CPM.log2.principal_components.pdf"/> 66 <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"/>
66 <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"/> 67 <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"/>
67 </output_collection> 68 </output_collection>
68 </test> 69 </test>
69 </tests> 70 </tests>
70 <help> 71 <help>