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comparison samples_qccheck.xml @ 9:934ac844f93d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 811337eaab815f54f0fd93a3dd23a1153993ea2a
author iuc
date Tue, 28 Jun 2016 12:22:27 -0400
parents a3d60df650b7
children
comparison
equal deleted inserted replaced
8:3cc94f4d58ae 9:934ac844f93d
7 </requirements> 7 </requirements>
8 <stdio> 8 <stdio>
9 <exit_code range="1:"/> 9 <exit_code range="1:"/>
10 </stdio> 10 </stdio>
11 <command><![CDATA[ 11 <command><![CDATA[
12 12
13 ln -s "${matrix}" "input.matrix" 13 ln -s "${matrix}" "input.matrix"
14 14
15 && 15 &&
16 16
17 PtR 17 PtR
18 --matrix "input.matrix" 18 --matrix "input.matrix"
19 19
20 --samples "${samples}" 20 --samples "${samples}"
21 21
22 --CPM --log2 --compare_replicates 22 --CPM --log2 --compare_replicates
23 23
24 && 24 &&
25 25
26 PtR 26 PtR
27 --matrix "input.matrix" 27 --matrix "input.matrix"
28 28
29 --samples "${samples}" 29 --samples "${samples}"
30 30
31 --CPM --log2 --sample_cor_matrix 31 --CPM --log2 --sample_cor_matrix
32 32
33 && 33 &&
34 34
35 PtR 35 PtR
36 --matrix "input.matrix" 36 --matrix "input.matrix"
37 37
38 --samples "${samples}" 38 --samples "${samples}"
39 39
40 --CPM --log2 --prin_comp 3 40 --CPM --log2 --prin_comp 3
41 41
42 && mkdir out_pdf 42 && mkdir out_pdf
43 && mv *rep_compare.pdf out_pdf/ 43 && mv *rep_compare.pdf out_pdf/
44 && mv *sample_cor_matrix.pdf out_pdf/ 44 && mv *sample_cor_matrix.pdf out_pdf/
45 && mv *principal_components.pdf out_pdf/ 45 && mv *principal_components.pdf out_pdf/
46 46
47 ]]></command> 47 ]]></command>
48 <inputs> 48 <inputs>
49 <param format="tabular" name="matrix" type="data" label="Expression matrix" help="output of abundance_estimates_to_matrix tool"/> 49 <param format="tabular" name="matrix" type="data" label="Expression matrix" help="output of abundance_estimates_to_matrix tool"/>
50 <param format="tabular" name="samples" type="data" label="Samples description" help="file describing samples and replicates"/> 50 <param format="tabular" name="samples" type="data" label="Samples description" help="file describing samples and replicates"/>
51 </inputs> 51 </inputs>
52 <outputs> 52 <outputs>
53 <collection name="reports" type="list" label="Quality check result files on ${on_string}"> 53 <collection name="reports" type="list" label="Quality check result files on ${on_string}">
54 <discover_datasets pattern="__name__" ext="pdf" directory="out_pdf" visible="true" /> 54 <discover_datasets pattern="__name__" ext="pdf" directory="out_pdf" />
55 </collection> 55 </collection>
56 </outputs> 56 </outputs>
57 <tests> 57 <tests>
58 <test> 58 <test>
59 <param name="matrix" value="count/qcheck/matrix.counts.matrix"/> 59 <param name="matrix" value="count/qcheck/matrix.counts.matrix"/>
104 104
105 105
106 .. _Trinity: http://trinityrnaseq.github.io 106 .. _Trinity: http://trinityrnaseq.github.io
107 ]]> 107 ]]>
108 </help> 108 </help>
109 109
110 <citations> 110 <citations>
111 <citation type="doi">10.1038/nbt.1883</citation> 111 <citation type="doi">10.1038/nbt.1883</citation>
112 </citations> 112 </citations>
113 </tool> 113 </tool>
114 114