Mercurial > repos > mvdbeek > tepid_merge_insertions
comparison tepid_merge_insertions.xml @ 0:6e4b5319cb89 draft default tip
planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
| author | mvdbeek |
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| date | Mon, 23 Jan 2017 10:05:12 -0500 |
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| -1:000000000000 | 0:6e4b5319cb89 |
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| 1 <tool id="tepid_merge_insertions" name="tepid-merge-insertions" version="@WRAPPER_VERSION@"> | |
| 2 <description>discover TE variants</description> | |
| 3 <macros> | |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements"/> | |
| 7 <version_command>tepid-discover --version</version_command> | |
| 8 <command detect_errors="exit_code"><![CDATA[ | |
| 9 #for $input in $insertions: | |
| 10 ln -s -f '$input' '$input.element_identifier' && | |
| 11 #end for | |
| 12 python '$__tool_directory__'/merge_insertions.py -i | |
| 13 #for $input in $insertions: | |
| 14 '$input.element_identifier' | |
| 15 #end for | |
| 16 -o '$merged_out' | |
| 17 ]]></command> | |
| 18 <inputs> | |
| 19 <param name="insertions" label="TEPID insertions" argument="--input" type="data_collection" format="bed"/> | |
| 20 </inputs> | |
| 21 <outputs> | |
| 22 <data name="merged_out" format="bed" label="tepid_discover merged insertions on ${on_string}"> | |
| 23 </data> | |
| 24 </outputs> | |
| 25 <tests> | |
| 26 <test> | |
| 27 <param name="insertions"> | |
| 28 <collection type="list"> | |
| 29 <element name="1" value="1.bed" /> | |
| 30 <element name="2" value="2.bed" /> | |
| 31 </collection> | |
| 32 </param> | |
| 33 <output name="merged_out" file="test.bed"/> | |
| 34 </test> | |
| 35 </tests> | |
| 36 <help><![CDATA[ | |
| 37 This step merges insertions found by tepid discover. | |
| 38 The output can be used as input in the tepid-refine step. | |
| 39 ]]></help> | |
| 40 <expand macro="citations"/> | |
| 41 </tool> |