Mercurial > repos > iuc > cnvkit_antitarget
comparison antitarget.xml @ 0:98086253a782 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
| author | iuc |
|---|---|
| date | Sun, 14 May 2023 20:08:55 +0000 |
| parents | |
| children | b52fa1df3bc4 |
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| -1:000000000000 | 0:98086253a782 |
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| 1 <tool id="cnvkit_antitarget" name="CNVkit Antitarget" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> | |
| 2 <description>lists the chromosomal coordinates for targeted resequencing</description> | |
| 3 <macros> | |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="xrefs"/> | |
| 7 <expand macro="requirements"/> | |
| 8 <command detect_errors="exit_code"><![CDATA[ | |
| 9 ln -s '$targets_file' ./capture.bed && | |
| 10 #if $access | |
| 11 ln -s '$access' ./access.bed && | |
| 12 #end if | |
| 13 cnvkit.py antitarget | |
| 14 ./capture.bed | |
| 15 #if $access | |
| 16 --access ./access.bed | |
| 17 #end if | |
| 18 #if str($avg_size) | |
| 19 --avg-size $avg_size | |
| 20 #end if | |
| 21 #if str($min_size) | |
| 22 --min-size $min_size | |
| 23 #end if | |
| 24 --output capture.antitarget.bed | |
| 25 ]]></command> | |
| 26 <inputs> | |
| 27 <param name="targets_file" type="data" format="bed" label="input BED or interval file" help="" /> | |
| 28 <param argument="--access" type="data" optional="true" format="bed" label=" Regions of accessible sequence on chromosomes" help="" /> | |
| 29 <param argument="--avg-size" optional="true" type="integer" label="Average size of antitarget bins" min="1" value="150000" help="" /> | |
| 30 <param argument="--min-size" optional="true" type="integer" label="Minimum size of antitarget bins" min="1" value="25000" help="" /> | |
| 31 </inputs> | |
| 32 <outputs> | |
| 33 <data name="out_capture_antitarget" format="bed" label="${tool.name} on ${on_string}: capture antitarget regions" from_work_dir="capture.antitarget.bed" /> | |
| 34 </outputs> | |
| 35 <tests> | |
| 36 <test expect_num_outputs="1"> | |
| 37 <param name="targets_file" ftype="bed" value="capture.bed" /> | |
| 38 <param name="access" ftype="bed" value="access-excludes.bed" /> | |
| 39 <output name="out_capture_antitarget" file="capture.antitarget.bed" /> | |
| 40 </test> | |
| 41 </tests> | |
| 42 <help><![CDATA[ | |
| 43 Given a “target” BED file that lists the chromosomal coordinates of the tiled | |
| 44 regions used for targeted resequencing, derive a BED file off-target/”antitarget” regions. | |
| 45 ]]></help> | |
| 46 <expand macro="citations" /> | |
| 47 </tool> |