Mercurial > repos > rmarenco > hubarchivecreator
view hubArchiveCreator.xml @ 6:816956489fe9 draft
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 20817d2bd61639d88226c9cd0392cea420ded222
author | rmarenco |
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date | Tue, 19 Jul 2016 01:19:57 -0400 |
parents | 1b653b332695 |
children | acc233161f50 |
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<tool id="hubArchiveCreator" name="Hub Archive Creator" version="2.0.2"> <description> This Galaxy tool permits to prepare your files to be ready for Assembly Hub visualization. </description> <requirements> <requirement type="package" version="312">ucsc_tools</requirement> <requirement type="package" version="0.0.1">gff3ToGenePred</requirement> <requirement type="package" version="0.0.1">gtfToGenePred</requirement> <requirement type="package" version="0.0.1">genePredToBed</requirement> <requirement type="package" version="1.2">samtools</requirement> <!-- Conda dependencies --> <requirement type="package" version="324">ucsc-gff3togenepred</requirement> <requirement type="package" version="324">ucsc-gtftogenepred</requirement> <requirement type="package" version="324">ucsc-genepredtobed</requirement> <requirement type="package" version="1.3.1">samtools</requirement> </requirements> <stdio> <regex match="^pass1" source="stderr" level="log" description="bedToBigBed"/> <!-- TODO: Add the case pass1 and 0 chroms --> <!-- TODO: Add the case pass2 and 0 records or 0 fields --> </stdio> <!-- Idea: python \ -augustus [parameters] \ -trfBig [parameters] --> <command detect_errors="exit_code"><![CDATA[ mkdir -p $output.extra_files_path; python $__tool_directory__/hubArchiveCreator.py #import json #set global data_parameter_dict = {} ## Function to retrieve the data of the inputs #def prepare_json($input_to_prepare, $order_index, $extra_data_dict={}) #set false_path = str($input_to_prepare) #set name = $input_to_prepare.name #set data_dict = {"name": $name} #silent data_dict.update($extra_data_dict) ## Add the ordering by taking the tool form indexes #silent $data_dict.update({"order_index": $order_index + 1}) #silent $data_parameter_dict.update({$false_path: $data_dict}) #end def #for $i, $f in enumerate( $format ) #if $f.formatChoice.format_select == "bam" --bam $f.formatChoice.BAM #set bam_index = $f.formatChoice.BAM.metadata.bam_index #silent $prepare_json($f.formatChoice.BAM, $i, {"index": $bam_index}) #end if #if $f.formatChoice.format_select == "bed" #if $f.formatChoice.bedChoice.bed_select == "bed" --bed $f.formatChoice.bedChoice.BED #silent $prepare_json($f.formatChoice.bedChoice.BED, $i) #end if #if $f.formatChoice.bedChoice.bed_select == "bed_simple_repeats_option" --bedSimpleRepeats $f.formatChoice.bedChoice.BED_simple_repeats #silent $prepare_json($f.formatChoice.bedChoice.BED_simple_repeats, $i) #end if #end if #if $f.formatChoice.format_select == "bigwig" --bigwig $f.formatChoice.BIGWIG #silent $prepare_json($f.formatChoice.BIGWIG, $i) #end if #if $f.formatChoice.format_select == "gff3" --gff3 $f.formatChoice.GFF3 #silent $prepare_json($f.formatChoice.GFF3, $i) #end if #if $f.formatChoice.format_select == "gtf" ## Add also GTF from Agustus? See https://github.com/ENCODE-DCC/kentUtils/issues/8 --gtf $f.formatChoice.GTF #silent $prepare_json($f.formatChoice.GTF, $i) #end if #end for ## Dump the final json #set all_data_json = json.dumps($data_parameter_dict) -f $Fasta_File --data_json '$all_data_json' -d $__tool_directory__ -e $output.files_path -o $output; ]]></command> <inputs> <param format="fasta" name="Fasta_File" type="data" label="Reference genome" /> <repeat name="format" title="Formats"> <conditional name="formatChoice"> <param name="format_select" type="select" label="Format"> <option value="bam" selected="true">BAM</option> <option value="bed">BED</option> <option value="bigwig">BIGWIG</option> <option value="gff3">GFF3</option> <option value="gtf">GTF</option> </param> <when value="bam"> <param format="bam" name="BAM" type="data" label="BAM File" /> </when> <when value="bigwig"> <param format="bigwig" name="BIGWIG" type="data" label="BIGWIG File" /> </when> <when value="gff3"> <param format="gff3" name="GFF3" type="data" label="GFF3 File" /> </when> <when value="gtf"> <param format="gtf" name="GTF" type="data" label="GTF File" /> </when> <when value="bed"> <conditional name="bedChoice"> <param name="bed_select" type="select" label="Bed Choice"> <option value="bed" selected="true">Generic BED</option> <option value="bed_simple_repeats_option">BED simple repeats</option> </param> <when value="bed"> <param format="bed" name="BED" type="data" label="Generic Bed File Choice" /> </when> <when value="bed_simple_repeats_option"> <param format="bed" name="BED_simple_repeats" type="data" label="Bed Simple Repeats (Bed4+12) File" /> </when> </conditional> </when> </conditional> </repeat> </inputs> <outputs> <data format="trackhub" name="output"/> </outputs> <tests> <!-- Can also use assert_command to test command --> <!-- Testing GFF3 input --> <test> <param name="Fasta_File" value="dbia3.fa"/> <repeat name="format"> <conditional name="formatChoice"> <param name="format_select" value="gff3"/> <param name="GFF3" value="augustusDbia3.gff3"/> </conditional> </repeat> <repeat name="format"> <param name="BED_simple_repeats" value="dbia3_trfBig_unsorted.bed"/> <!-- TODO: Ask why the tests are not passing with this xml: Error creating a job for these tool inputs - Error executing tool: 'NoneType' object has no attribute 'current_history' <conditional name="formatChoice"> <param name="format_select" value="bed"/> <conditional name="bedChoice"> <param name="bed_select" value="bed_simple_repeats_option"/> <param name="BED_simple_repeats" value="dbia3_trfBig_unsorted.bed"/> </conditional> </conditional> --> </repeat> <output name="output"> <assert_contents> <has_text text="myHub"/> </assert_contents> <assert_contents> <has_text text="dbia3_trfBig.bb"/> </assert_contents> <assert_contents> <has_text text="SAODOAii qwwqod92921"/> </assert_contents> </output> </test> <test> <param name="Fasta_File" value="dbia3.fa"/> <param name="GFF3" value="augustusDbia3.gff3"/> <output name="output" file="augustusOutput.html" lines_diff="2"> <extra_files type="directory" value="myHub"/> <extra_files type="file" name="myHub/dbia3/tracks/augustusDbia3.bb" value="augustusDbia3.bb"/> </output> </test> <!-- Testing Generic BED input --> <!-- Testing Bed Simple repeat input --> </tests> <help> This Galaxy tool permits to prepare your files to be ready for Assembly Hub visualization. </help> </tool>