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view merge.xml @ 4:a2f62c0c0537 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/merge commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
author | devteam |
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date | Fri, 18 Dec 2015 19:39:00 -0500 |
parents | 1e9d95cae35f |
children | dfbbc0291b36 |
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<tool id="gops_merge_1" name="Merge" version="1.0.0"> <description>the overlapping intervals of a dataset</description> <requirements> <requirement type="package" version="0.7.1">bx-python</requirement> <requirement type="package" version="1.0.0">galaxy-ops</requirement> </requirements> <command interpreter="python">gops_merge.py $input1 $output -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol} $returntype</command> <inputs> <param format="interval" name="input1" type="data"> <label>Merge overlaping regions of</label> </param> <param name="returntype" type="boolean" truevalue="-3" falsevalue=""> <label>Output 3 column bed</label> </param> </inputs> <outputs> <data format="input" name="output" metadata_source="input1" /> </outputs> <code file="operation_filter.py"> <hook exec_after_process="exec_after_merge" /> </code> <tests> <test> <param name="input1" value="1.bed" /> <output name="output" file="gops-merge.dat" /> <param name="returntype" value="true" /> </test> <test> <param name="input1" value="2_mod.bed" ftype="interval"/> <output name="output" file="gops_merge_diffCols.dat" /> <param name="returntype" value="true" /> </test> <test> <param name="input1" value="gops_bigint.interval" /> <output name="output" file="gops_merge_out2.bed" /> <param name="returntype" value="true" /> </test> </tests> <help> .. class:: infomark **TIP:** If your dataset does not appear in the pulldown menu, it means that it is not in interval format. Use "edit attributes" to set chromosome, start, end, and strand columns. ----- **Screencasts!** See Galaxy Interval Operation Screencasts_ (right click to open this link in another window). .. _Screencasts: http://wiki.g2.bx.psu.edu/Learn/Interval%20Operations ----- This operation merges all overlapping intervals into single intervals. **Example** .. image:: gops_merge.gif </help> </tool>