Mercurial > repos > yating-l > jbrowsearchivecreator
diff jbrowse_hub.xml @ 0:804a93e87cc8 draft
planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
| author | yating-l |
|---|---|
| date | Wed, 12 Apr 2017 17:41:55 -0400 |
| parents | |
| children | ac83821b0e06 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/jbrowse_hub.xml Wed Apr 12 17:41:55 2017 -0400 @@ -0,0 +1,293 @@ +<tool id="jbrowse_hub" name="JBrowse Hub Creator" version="1.0"> + <description> + This Galaxy tool is used to prepare your files to be ready for displaying on JBrowse + </description> + + <requirements> + <requirement type="package" version="1.2">samtools</requirement> + <requirement type="package" version="1.9">numpy</requirement> + <requirement type="package" version="1.68">biopython</requirement> + <requirement type="package" version="1.0">ucsc_tools_340</requirement> + <requirement type="package" version="1.12.1">jbrowse_tools</requirement> + </requirements> + + <stdio> + </stdio> + + <command detect_errors="exit_code"><![CDATA[ + python $__tool_directory__/jbrowse_hub.py + --fasta '$reference' + --genome_name '$genome_name' + + #set galaxy_url = str($GALAXY_URL) + #set $jbrowse_url = galaxy_url.replace("8080", "80") + --jbrowse_host '$jbrowse_url' + + ## json metadata recording from Remi's hub-archive-creator.xml + #import json + #set global data_parameter_dict = {} + + ## Function to retrieve the data of the inputs + #def prepare_json($input_to_prepare, $extra_data_dict={}) + #set false_path = str($input_to_prepare) + #set name = $input_to_prepare.name + + #set data_dict = {"name": $name} + #silent data_dict.update($extra_data_dict) + + #silent $data_parameter_dict.update({$false_path: $data_dict}) + + #end def + + #for $g in $group + #for $f in $g.format + #set track_label = str($f.formatChoice.label) + #set group_name = str($g.group_name) + #set extra_data_dict = {"label" : $track_label, "category" : $group_name} + #if $f.formatChoice.format_select == 'bed' + #set track_color = str($f.formatChoice.track_color) + #silent extra_data_dict.update({"color" : $track_color}) + #if $f.formatChoice.bedChoice.bed_select == 'bed_generic_option' + --bed $f.formatChoice.bedChoice.BED_generic + #silent $prepare_json($f.formatChoice.bedChoice.BED_generic, extra_data_dict) + #elif $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, extra_data_dict) + #elif $f.formatChoice.bedChoice.bed_select == 'bed_splice_junctions_option' + --bedSpliceJunctions $f.formatChoice.bedChoice.BED_splice_junctions + #silent $prepare_json($f.formatChoice.bedChoice.BED_splice_junctions, extra_data_dict) + #end if + #end if + #if $f.formatChoice.format_select == 'bam' + --bam $f.formatChoice.BAM + #silent $prepare_json($f.formatChoice.BAM, extra_data_dict) + #end if + #if $f.formatChoice.format_select == 'gff3' + #set track_color = str($f.formatChoice.track_color) + #silent extra_data_dict.update({"color" : $track_color}) + #if $f.formatChoice.gff3Choice.gff3_select == 'gff3_generic' + --gff3 $f.formatChoice.gff3Choice.GFF3_generic + #silent $prepare_json($f.formatChoice.gff3Choice.GFF3_generic, extra_data_dict) + #elif $f.formatChoice.gff3Choice.gff3_select == 'gff3_transcript' + --gff3_transcript $f.formatChoice.gff3Choice.GFF3_transcript + #silent $prepare_json($f.formatChoice.gff3Choice.GFF3_transcript, extra_data_dict) + #elif $f.formatChoice.gff3Choice.gff3_select == 'gff3_mrna' + --gff3_mrna $f.formatChoice.gff3Choice.GFF3_mrna + #silent $prepare_json($f.formatChoice.gff3Choice.GFF3_mrna, extra_data_dict) + #end if + #end if + #if $f.formatChoice.format_select == 'blastxml' + --blastxml $f.formatChoice.BlastXML + #silent $prepare_json($f.formatChoice.BlastXML, extra_data_dict) + #end if + #if $f.formatChoice.format_select == 'gtf' + --gtf $f.formatChoice.GTF + #set track_color = str($f.formatChoice.track_color) + #silent extra_data_dict.update({"color" : $track_color}) + #silent $prepare_json($f.formatChoice.GTF, extra_data_dict) + #end if + #if $f.formatChoice.format_select == 'bigwig' + --bigwig $f.formatChoice.BIGWIG + #set pos_color = str($f.formatChoice.pos_color) + #set neg_color = str($f.formatChoice.neg_color) + #silent $extra_data_dict.update({"style" : {"pos_color" : $pos_color, "neg_color" : $neg_color}}) + #silent $prepare_json($f.formatChoice.BIGWIG, extra_data_dict) + #end if + #end for + #end for + + #set all_data_json = json.dumps($data_parameter_dict) + -j '$all_data_json' + -e '$output.extra_files_path' + -o '$output' + + ]]></command> + + <inputs> + <param name="GALAXY_URL" type="baseurl" value="" /> + <param name="reference" type="data" format="fasta" label="Reference Genome" /> + <param name="genome_name" type="text" size="30" value="unknown" label="Genome name" /> + <repeat name="group" title="New group"> + <param type="text" name="group_name" label="Group name" value="Default group"/> + <repeat name="format" title="New track"> + <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="blastxml">BLASTXML</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" + /> + <param name="label" type="text" size="30" value = "Sequence Alignment" label="Track name" /> + </when> + <when value="bed"> + <conditional name="bedChoice"> + <param name="bed_select" type="select" label="Bed Choice"> + <option value="bed_generic_option">BED format</option> + <option value="bed_simple_repeats_option">BED Simple repeat (bed4+12 / simpleRepeat.as)</option> + <option value="bed_splice_junctions_option">BED Splice junctions (bed12+1 / spliceJunctions.as)</option> + </param> + <when value="bed_generic_option"> + <param + format="bed" + name="BED_generic" + type="data" + label="Bed File" + /> + </when> + <when value="bed_simple_repeats_option"> + <param + format="bed" + name="BED_simple_repeats" + type="data" + label="Bed Simple Repeats (Bed4+12) File" + /> + </when> + <when value="bed_splice_junctions_option"> + <param + format="bed" + name="BED_splice_junctions" + type="data" + label="Bed Splice Junctions (Bed12+1) File" + /> + </when> + </conditional> + <param name="label" type="text" size="30" value="BED file" label="Track name" /> + <param name="track_color" type="color" label="Track color" value="#daa520"> + <sanitizer> + <valid initial="string.letters,string.digits"> + <add value="#"/> + </valid> + </sanitizer> + </param> + </when> + <when value="blastxml"> + <param + format="blastxml" + name="BlastXML" + type="data" + label="Blast Alignments File" + /> + <param name="label" type="text" size="30" value="Blast Alignment" label="Track name" /> + </when> + <when value="bigwig"> + <param + format="bigwig" + name="BIGWIG" + type="data" + label="BIGWIG File" + /> + <param name="label" type="text" size="30" value="Sequence Coverage" label="Track name" /> + <param name="pos_color" type="color" label="Positive Coverage Color" value="#FFA600"> + <sanitizer> + <valid initial="string.letters,string.digits"> + <add value="#"/> + </valid> + </sanitizer> + </param> + <param name="neg_color" type="color" label="Negative Coverage Color" value="#005EFF"> + <sanitizer> + <valid initial="string.letters,string.digits"> + <add value="#"/> + </valid> + </sanitizer> + </param> + </when> + <when value="gff3"> + <conditional name="gff3Choice"> + <param name="gff3_select" type="select" label="gff3 type"> + <option value="gff3_generic">GFF3 format</option> + <option value="gff3_transcript">GFF3 format output from gene prediction tools (e.g. Augustus), structure: gene->transcription->CDS</option> + <option value="gff3_mrna">GFF3 format output from gene prediction tools (e.g. SNAP), structure: gene->mRNA->CDS</option> + </param> + <when value="gff3_generic"> + <param + format="gff3" + name="GFF3_generic" + type="data" + label="GFF3 File" + /> + </when> + <when value="gff3_transcript"> + <param + format="gff3" + name="GFF3_transcript" + type="data" + label="GFF3 File from gene prediction" + /> + </when> + <when value="gff3_mrna"> + <param + format="gff3" + name="GFF3_mrna" + type="data" + label="GFF3 File from gene prediction" + /> + </when> + </conditional> + <param name="label" type="text" size="30" value="Gene Prediction" label="Track name" /> + <param name="track_color" type="color" label="Track color" value="#daa520"> + <sanitizer> + <valid initial="string.letters,string.digits"> + <add value="#"/> + </valid> + </sanitizer> + </param> + </when> + <when value="gtf"> + <param + format="gtf" + name="GTF" + type="data" + label="GTF File" + /> + <param name="label" type="text" size="30" value="Assembled Transcripts" label="Track name" /> + <param name="track_color" type="color" label="Track color" value="#daa520"> + <sanitizer> + <valid initial="string.letters,string.digits"> + <add value="#"/> + </valid> + </sanitizer> + </param> + </when> + </conditional> + </repeat> + </repeat> + </inputs> + + <outputs> + <data format="html" name="output" label="${tool.name}" /> + </outputs> + <tests> + <test> + <param name="reference" value="dbia3/raw/dbia3.fa" /> + <param name="output" value="hubtest" /> + <repeat name="group"> + <param name="group_name" value="Default group"/> + <repeat name="format"> + <conditional name="formatChoice"> + <param name="format_select" value="gff3_transcript"/> + <param name="GFF3_transcript" value="dbia3/raw/Augustus_on_data_3__GTF_GFF.gff3" /> + </conditional> + </repeat> + </repeat> + <output name="output" file="hubtest" > + </output> + </test> + </tests> + <help> + This Galaxy tool will create a tar file which including raw datasets and json datasets that can be used for + JBrowse visualization. + </help> + <citations> + </citations> +</tool> \ No newline at end of file