Mercurial > repos > trinity_ctat > ctat_concatenate
comparison ctat_concatenate.xml @ 0:702a3586942a draft default tip
Upload ctat tools.
| author | trinity_ctat |
|---|---|
| date | Tue, 17 Jul 2018 11:48:23 -0400 |
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| -1:000000000000 | 0:702a3586942a |
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| 1 <tool id="ctat_concatenate" name="ctat_concatenate" version="1.0.0" profile="17.05"> | |
| 2 <description> concatenate datasets from tail to head</description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="2.7">python</requirement> | |
| 5 </requirements> | |
| 6 | |
| 7 <command detect_errors="exit_code"> | |
| 8 <![CDATA[ | |
| 9 python $__tool_directory__/ctat_bash_command_executer.py cat | |
| 10 $input1 | |
| 11 #for $q in $queries | |
| 12 ${q.input2} | |
| 13 #end for | |
| 14 > $out_file1 | |
| 15 ]]> | |
| 16 </command> | |
| 17 <inputs> | |
| 18 <param name="input1" type="data" label="Concatenate Dataset"/> | |
| 19 <repeat name="queries" title="Dataset"> | |
| 20 <param name="input2" type="data" label="Select" /> | |
| 21 </repeat> | |
| 22 </inputs> | |
| 23 <outputs> | |
| 24 <data name="out_file1" format="input" metadata_source="input1"/> | |
| 25 </outputs> | |
| 26 | |
| 27 <tests> | |
| 28 <test> | |
| 29 <param name="input1" value="Sp_ds.left.fq"/> | |
| 30 <param name="input2" value="Sp_hs.left.fq"/> | |
| 31 <output name="out_file1" file="Sp.cat_ds_hs.left.fq"> | |
| 32 <assert_contents> | |
| 33 <has_line_matching expression=".+" /> | |
| 34 </assert_contents> | |
| 35 </output> | |
| 36 </test> | |
| 37 <test> | |
| 38 <param name="input1" value="Sp_ds.right.fq"/> | |
| 39 <param name="input2" value="Sp_hs.right.fq"/> | |
| 40 <output name="out_file1" file="Sp.cat_ds_hs.right.fq"> | |
| 41 <assert_contents> | |
| 42 <has_line_matching expression=".+" /> | |
| 43 </assert_contents> | |
| 44 </output> | |
| 45 </test> | |
| 46 <!--TODO: if possible, enhance the underlying test code to handle this test | |
| 47 the problem is multiple params with the same name "input2" | |
| 48 <test> | |
| 49 <param name="input1" value="1.bed"/> | |
| 50 <param name="input2" value="2.bed"/> | |
| 51 <param name="input2" value="3.bed"/> | |
| 52 <output name="out_file1" file="cat_wrapper_out2.bed"/> | |
| 53 </test> | |
| 54 --> | |
| 55 </tests> | |
| 56 <help> | |
| 57 .. class:: infomark | |
| 58 | |
| 59 Combine left and right reads of paired ends for different conditions into a single target for Trinity assembly. | |
| 60 | |
| 61 If you are following the Trinity RNA-seq protocol please go here_ for a galaxy tool walk through or the Nature Protocols paper_. | |
| 62 | |
| 63 .. _here: https://github.com/trinityrnaseq/GalaxyTrinityProtocol/wiki | |
| 64 .. _paper: http://www.nature.com/nprot/journal/v8/n8/full/nprot.2013.084.html | |
| 65 </help> | |
| 66 </tool> |