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comparison cummeRbund_macros.xml @ 0:e462121e8269 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
author devteam
date Mon, 09 Nov 2015 11:27:38 -0500
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children aefbcaf15a94
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-1:000000000000 0:e462121e8269
1 <?xml version="1.0"?>
2 <macros>
3 <macro name="stdio">
4 <stdio>
5 <exit_code range="1:" />
6 <exit_code range=":-1" />
7 <regex match="Error:" />
8 <regex match="Exception:" />
9 </stdio>
10 </macro>
11 <macro name="replicates_checkbox">
12 <param name="replicates" type="boolean" truevalue="--replicates" falsevalue="" checked="True" label="Replicates?"/>
13 </macro>
14 <macro name="log10_checkbox">
15 <param name="log10" type="boolean" truevalue="--log10" falsevalue="" checked="True" label="Apply log10 transformation on FPKM values?"/>
16 </macro>
17 <macro name="xy_selector">
18 <param name="x" type="select" label="Sample name for x axis" dynamic_options="get_samples(input_database.dataset.file_name)" />
19 <param name="y" type="select" label="Sample name for y axis" dynamic_options="get_samples(input_database.dataset.file_name)" />
20 </macro>
21 <macro name="genes_selector">
22 <repeat name="genes" title="Genes">
23 <param name="gene_id" type="select" label="Gene ID" dynamic_options="get_genes(input_database.dataset.file_name)" />
24 </repeat>
25 </macro>
26 <macro name="features_selector">
27 <param name="features" type="select" label="Expression levels to plot?">
28 <option value="gene" selected="true">Genes</option>
29 <option value="isoforms">Isoforms</option>
30 <option value="tss">TSS</option>
31 <option value="cds">CDS</option>
32 </param>
33 </macro>
34 <macro name="multiple_genes_conditional">
35 <conditional name="multiple_genes">
36 <param name="multiple_genes_selector" type="select" label="Limit plot to genes">
37 <option value="no" selected="true">Do not limit</option>
38 <option value="yes">Select genes</option>
39 </param>
40 <when value="yes">
41 <expand macro="features_selector" />
42 <expand macro="genes_selector" />
43 </when>
44 <when value="no" />
45 </conditional>
46 </macro>
47 </macros>