Mercurial > repos > iuc > cnvkit_access
comparison access.xml @ 0:22878d2aff05 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
| author | iuc |
|---|---|
| date | Sun, 14 May 2023 20:09:17 +0000 |
| parents | |
| children | 9f18bcf53f92 |
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| -1:000000000000 | 0:22878d2aff05 |
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| 1 <tool id="cnvkit_access" name="CNVkit Access" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> | |
| 2 <description>Calculate the sequence-accessible coordinates in chromosomes</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 #import re | |
| 10 ln -s '$fa_fname' ./genome.fasta && | |
| 11 #if $exclude | |
| 12 #set $names = [] | |
| 13 #set $x=1 | |
| 14 #for $x, $exc in enumerate($exclude): | |
| 15 #set $name_base = re.sub('[^\w\-_\.]', '_', $exc.element_identifier) | |
| 16 #set $name = $name_base + '_' + str(x) | |
| 17 #silent $names.append( $name ) | |
| 18 ln -s '$exc' ${name}.bed && | |
| 19 #end for | |
| 20 #end if | |
| 21 cnvkit.py access | |
| 22 ./genome.fasta | |
| 23 #if $exclude | |
| 24 #for $name in $names: | |
| 25 --exclude ${name}.bed | |
| 26 #end for | |
| 27 #end if | |
| 28 #if str($min_gap_size) | |
| 29 --min-gap-size $min_gap_size | |
| 30 #end if | |
| 31 --output access-excludes.bed | |
| 32 ]]></command> | |
| 33 <inputs> | |
| 34 <param name="fa_fname" type="data" format="fasta" label="Target coverage file" help="Reference genome fasta file" /> | |
| 35 <param argument="--min-gap-size" optional="true" type="integer" label="Minimum gap size between accessible sequence regions" min="0" value="5000" help="Regions separated by less than this distance will be joined together" /> | |
| 36 <param argument="--exclude" type="data" optional="true" format="bed" multiple="true" label="Additional regions to exclude" help="" /> | |
| 37 </inputs> | |
| 38 <outputs> | |
| 39 <data name="out_sample_access" format="bed" label="${tool.name} on ${on_string}: Sequence-accessible coordinates" from_work_dir="access-excludes.bed" /> | |
| 40 </outputs> | |
| 41 <tests> | |
| 42 <test expect_num_outputs="1"> | |
| 43 <param name="fa_fname" ftype="fasta" value="genome.fasta" /> | |
| 44 <param name="min_gap_size" value="2500" /> | |
| 45 <param name="exclude" ftype="bed" value="excludes.bed" /> | |
| 46 <output name="out_sample_access" file="access-excludes.bed" /> | |
| 47 </test> | |
| 48 <test expect_num_outputs="1"> | |
| 49 <param name="fa_fname" ftype="fasta" value="genome.fasta" /> | |
| 50 <param name="min_gap_size" value="2500" /> | |
| 51 <param name="exclude" ftype="bed" value="excludes.bed,excludes_1.bed" /> | |
| 52 <output name="out_sample_access" file="access-excludes.bed" /> | |
| 53 </test> | |
| 54 </tests> | |
| 55 <help><![CDATA[ | |
| 56 The access command computes the locations of the accessible sequence regions for a given reference genome | |
| 57 based on these masked-out sequences, treating long spans of ‘N’ characters as the inaccessible regions | |
| 58 and outputting the coordinates of the regions between them. | |
| 59 ]]></help> | |
| 60 <expand macro="citations" /> | |
| 61 </tool> |