Mercurial > repos > rmarenco > hubarchivecreator
changeset 0:0f3bc17e5ede draft
Uploaded
| author | rmarenco |
|---|---|
| date | Wed, 13 Jul 2016 13:22:54 -0400 |
| parents | |
| children | fb5e60d4d18a |
| files | hubArchiveCreator.xml |
| diffstat | 1 files changed, 227 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/hubArchiveCreator.xml Wed Jul 13 13:22:54 2016 -0400 @@ -0,0 +1,227 @@ +<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>