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comparison concatenate.xml @ 0:7a974f285033 draft

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Initial commit with concatenate and trinity tools. Still testing.
author trinity_ctat
date Mon, 11 Sep 2017 16:40:43 -0400
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children 1e638acde0cf
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-1:000000000000 0:7a974f285033
1 <tool id="catbash" name="Concatenate datasets">
2 <description> concatenate datasets from tail to head</description>
3 <command interpreter="python">
4 bash_command_executer.py cat
5 $input1
6 #for $q in $queries
7 ${q.input2}
8 #end for
9 > $out_file1
10 </command>
11 <inputs>
12 <param name="input1" type="data" label="Concatenate Dataset"/>
13 <repeat name="queries" title="Dataset">
14 <param name="input2" type="data" label="Select" />
15 </repeat>
16 </inputs>
17 <outputs>
18 <data name="out_file1" format="input" metadata_source="input1"/>
19 </outputs>
20 <tests>
21 <test>
22 <param name="input1" value="Sp_ds.left.fq"/>
23 <param name="input2" value="Sp_hs.left.fq"/>
24 <output name="out_file1" file="Sp.cat_ds_hs.left.fq">
25 <assert_contents>
26 <has_line_matching expression=".+" />
27 </assert_contents>
28 </output>
29 </test>
30 <test>
31 <param name="input1" value="Sp_ds.right.fq"/>
32 <param name="input2" value="Sp_hs.right.fq"/>
33 <output name="out_file1" file="Sp.cat_ds_hs.right.fq">
34 <assert_contents>
35 <has_line_matching expression=".+" />
36 </assert_contents>
37 </output>
38 </test>
39 <!--TODO: if possible, enhance the underlying test code to handle this test
40 the problem is multiple params with the same name "input2"
41 <test>
42 <param name="input1" value="1.bed"/>
43 <param name="input2" value="2.bed"/>
44 <param name="input2" value="3.bed"/>
45 <output name="out_file1" file="cat_wrapper_out2.bed"/>
46 </test>
47 -->
48 </tests>
49 <help>
50 .. class:: infomark
51
52 Combine left and right reads of paired ends for different conditions into a single target for Trinity assembly.
53
54 If you are following the Trinity RNA-seq protocol please go here_ for a galaxy tool walk through or the Nature Protocols paper_.
55
56 .. _here: https://github.com/trinityrnaseq/GalaxyTrinityProtocol/wiki
57 .. _paper: http://www.nature.com/nprot/journal/v8/n8/full/nprot.2013.084.html
58 </help>
59 </tool>