Mercurial > repos > yating-l > hubarchivecreator
diff hubArchiveCreator.xml @ 0:f493979f1408 draft default tip
planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test commit 48b59e91e2dcc2e97735ee35d587960cbfbce932-dirty
| author | yating-l |
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| date | Wed, 21 Dec 2016 12:13:04 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/hubArchiveCreator.xml Wed Dec 21 12:13:04 2016 -0500 @@ -0,0 +1,1014 @@ +<tool id="hubArchiveCreator" name="Hub Archive Creator" version="2.3.0"> + <description> + This Galaxy tool permits to prepare your files to be ready for + Assembly Hub visualization. + </description> + + <requirements> + <!-- Conda dependencies --> + <requirement type="package" version="332">ucsc-bedtobigbed</requirement> + <requirement type="package" version="332">ucsc-fatotwobit</requirement> + <requirement type="package" version="332">ucsc-genepredtobed</requirement> + <requirement type="package" version="332">ucsc-genepredtobiggenepred</requirement> + <requirement type="package" version="332">ucsc-gff3togenepred</requirement> + <requirement type="package" version="332">ucsc-gtftogenepred</requirement> + <!-- TODO: Change the conda ucsc-psltobigpsl and take one > v337 because of bugs before --> + <!-- <requirement type="package" version="332">ucsc-psltobigpsl</requirement> --> + <requirement type="package" version="332">ucsc-twobitinfo</requirement> + <requirement type="package" version="1.3">samtools</requirement> + <!-- ToolShed dependencies --> + <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="0.0.1">genePredToBigGenePred</requirement> + <requirement type="package" version="0.0.1">pslToBigPsl</requirement> + <requirement type="package" version="1.2">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 $__tool_directory__/hubArchiveCreator.py + + ## Ask the user to enter the genome name + --genome_name '$genome_name' + + #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}) + + #silent $data_parameter_dict.update({$false_path: $data_dict}) + + #end def + + + ## Get the number of digits from tracks, to have a unique integer from group index and track index + + #set temp_max_digit = 0 + + #for $g in $group + #if len($g.format) > $temp_max_digit + #silent temp_max_digit = len($g.format) + #end if + #end for + + #set nb_digits_max_track = len(str($temp_max_digit)) + + ## END Get the number of digits + + #for $i_g, $g in enumerate( $group ) + #for $i, $f in enumerate( $g.format ) + ## Create the order index using index_group+1 concatenated with index_track + #set index_group_final = str($i_g + 1) + #set index_track_final = str($index_group_final) + str($i).zfill($nb_digits_max_track) + + ## For each format, we have a few mandatory fields we store in a dict + #set track_color = str($f.formatChoice.track_color) + #set group_name = str($g.group_name) + + #set extra_data_dict = {"track_color": $track_color, + "group_name": $group_name} + + #if $f.formatChoice.format_select == "bam" + --bam $f.formatChoice.BAM + #set bam_index = $f.formatChoice.BAM.metadata.bam_index + + ## Add Bam format specific fields + #silent extra_data_dict.update({"index": $bam_index}) + + #silent $prepare_json($f.formatChoice.BAM, $index_track_final, extra_data_dict) + #end if + #if $f.formatChoice.format_select == "bed" + #if $f.formatChoice.bedChoice.bed_select == "bed_generic" + --bed $f.formatChoice.bedChoice.BED + #silent $prepare_json($f.formatChoice.bedChoice.BED, $index_track_final, + extra_data_dict) + #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, $index_track_final, + extra_data_dict) + #end if + #if $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, $index_track_final, + extra_data_dict) + #end if + #end if + #if $f.formatChoice.format_select == "psl" + --psl $f.formatChoice.PSL + #silent $prepare_json($f.formatChoice.PSL, $index_track_final, + extra_data_dict) + #end if + #if $f.formatChoice.format_select == "bigwig" + --bigwig $f.formatChoice.BIGWIG + #silent $prepare_json($f.formatChoice.BIGWIG, $index_track_final, + extra_data_dict) + #end if + #if $f.formatChoice.format_select == "gff3" + --gff3 $f.formatChoice.GFF3 + #silent $prepare_json($f.formatChoice.GFF3, $index_track_final, + extra_data_dict) + #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, $index_track_final, + extra_data_dict) + #end if + #end for + #end for + + ## We combine the fasta file dataset name with his false path in a JSON object + #set fasta_json = json.dumps({"false_path": str($fasta_file), "name": $fasta_file.name}) + -f '$fasta_json' + + ## Dump the final json + #set all_data_json = json.dumps($data_parameter_dict) + + --data_json '$all_data_json' + + ## Retrieve the user email + --user_email $__user_email__ + + -d $__tool_directory__ + + -e $output.extra_files_path + + $advanced_options.debug_mode + + -o $output; + + ]]></command> + + <inputs> + <param + name="genome_name" + type="text" + size="30" + value="unknown" + label="UCSC Genome Browser assembly ID" + /> + <param + format="fasta" + name="fasta_file" + type="data" + label="Reference genome" + /> + <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="psl">PSL</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" + /> + <!-- TODO: Find a solution to avoid repetition and to generate a new color depending on the others --> + <param name="track_color" type="color" label="Track color" value="#000000"> + <sanitizer> + <valid initial="string.letters,string.digits"> + <add value="#"/> + </valid> + </sanitizer> + </param> + </when> + <when value="bed"> + <conditional name="bedChoice"> + <param name="bed_select" type="select" label="Bed Choice"> + <option value="bed_generic" selected="true">BED Generic (bed3+)</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"> + <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> + <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="track_color" type="color" label="Track color" value="#000000"> + <sanitizer> + <valid initial="string.letters,string.digits"> + <add value="#"/> + </valid> + </sanitizer> + </param> + </when> + <when value="psl"> + <param + format="psl" + name="PSL" + type="data" + label="PSL File" + /> + <param name="track_color" type="color" label="Track color" value="#000000"> + <sanitizer> + <valid initial="string.letters,string.digits"> + <add value="#"/> + </valid> + </sanitizer> + </param> + </when> + <when value="bigwig"> + <param + format="bigwig" + name="BIGWIG" + type="data" + label="BIGWIG File" + /> + <param name="track_color" type="color" label="Track color" value="#000000"> + <sanitizer> + <valid initial="string.letters,string.digits"> + <add value="#"/> + </valid> + </sanitizer> + </param> + </when> + <when value="gff3"> + <param + format="gff3" + name="GFF3" + type="data" + label="GFF3 File" + /> + <param name="track_color" type="color" label="Track color" value="#000000"> + <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="track_color" type="color" label="Track color" value="#000000"> + <sanitizer> + <valid initial="string.letters,string.digits"> + <add value="#"/> + </valid> + </sanitizer> + </param> + </when> + </conditional> + </repeat> + </repeat> + <conditional name="advanced_options"> + <param name="advanced_options_selector" type="select" label="Advanced options"> + <option value="off" selected="true">Hide advanced options</option> + <option value="on">Display advanced options</option> + </param> + <!-- TODO: Avoid redundancy here --> + <when value="on"> + <param name="debug_mode" type="boolean" + label="Activate debug mode" checked="false" + truevalue="--debug_mode" falsevalue=""> + <help> + Use this option if you are a G-OnRamp developer + </help> + </param> + </when> + <when value="off"> + <param name="debug_mode" type="hidden" + value=""> + </param> + </when> + </conditional> +</inputs> + + <outputs> + <data format="trackhub" name="output"/> + </outputs> + + <tests> + <!-- Test with only the fasta file --> + <test> + <param name="genome_name" value="Dbia3"/> + <param name="fasta_file" value="common/dbia3.fa"/> + <output name="output" file="only_genome/only_genome.html"> + <extra_files type="file" name="__main__.log" value="only_genome/__main__.log" /> + <extra_files type="file" name="myHub/genomes.txt" value="only_genome/myHub/genomes.txt" /> + <extra_files type="file" name="myHub/Dbia3.html" value="only_genome/myHub/Dbia3.html"/> + <!-- Email could be different, but we need to ensure we still have the email line --> + <extra_files type="file" name="myHub/hub.txt" value="only_genome/myHub/hub.txt" lines_diff="2"> + <assert_contents> + <has_text text="email"/> + </assert_contents> + </extra_files> + <extra_files type="file" name="myHub/Dbia3/Dbia3.2bit" value="common/Dbia3.2bit"> + </extra_files> + <extra_files type="file" name="myHub/Dbia3/description.html" value="only_genome/myHub/Dbia3/description.html"/> + </output> + </test> + + <!-- Test with Bam --> + <test> + <param name="genome_name" value="Dbia3"/> + <param name="fasta_file" value="common/dbia3.fa"/> + <repeat name="group"> + <param name="group_name" value="Default group"/> + <repeat name="format"> + <conditional name="formatChoice"> + <param name="format_select" value="bam"/> + <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam" /> + <param name="track_color" value="#000000"/> + </conditional> + </repeat> + </repeat> + <output name="output" file="bam/bam.html"> + <!-- Verify tracks folder contains bam and bai --> + <extra_files type="file" + name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam" + value="bam/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam" + compare="sim_size" + /> + <extra_files type="file" + name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai" + value="bam/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai" + compare="sim_size" + /> + <!-- Verify trackDb.txt contains the basic fields for a bam --> + <extra_files type="file" name="myHub/Dbia3/trackDb.txt" value="bam/myHub/Dbia3/trackDb.txt"> + <assert_contents> + <has_text text="track"/> + <has_text text="longLabel"/> + <has_text text="shortLabel"/> + <has_text text="bigDataUrl"/> + <has_text text="type"/> + <has_text text="visibility"/> + <has_text text="thickDrawItem"/> + <has_text text="priority"/> + <has_text text="color"/> + <has_text text="group"/> + </assert_contents> + </extra_files> + <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition --> + </output> + </test> + + <!-- Test with Bed Generic --> + <test> + <param name="genome_name" value="Dbia3"/> + <param name="fasta_file" value="common/dbia3.fa"/> + <repeat name="group"> + <param name="group_name" value="Default group"/> + <repeat name="format"> + <conditional name="formatChoice"> + <param name="format_select" value="bed" /> + <conditional name="bedChoice"> + <param name="bed_select" value="bed_generic"/> + <param name="BED" ftype="bed" value="bed_generic/inputs/TBLASTN_Alignment_to_proteins"/> + <param name="track_color" value="#000000"/> + </conditional> + </conditional> + </repeat> + </repeat> + <output name="output" file="bed_generic/bed_generic.html"> + <!-- Verify tracks folder contains bam and bai --> + <extra_files type="file" + name="myHub/Dbia3/tracks/TBLASTN_Alignment_to_proteins.bb" + value="bed_generic/myHub/Dbia3/tracks/TBLASTN_Alignment_to_proteins.bb" + compare="sim_size" + /> + </output> + </test> + + <!-- Test with Bed Simple repeat --> + <test> + <param name="genome_name" value="Dbia3"/> + <param name="fasta_file" value="common/dbia3.fa"/> + <repeat name="group"> + <param name="group_name" value="Default group"/> + <repeat name="format"> + <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" ftype="bed" value="bed_simple_repeats/inputs/Repeating_Elements_by_TrfBig"/> + <param name="track_color" value="#000000"/> + </conditional> + </conditional> + </repeat> + </repeat> + <output name="output" file="bed_simple_repeats/bed_simple_repeats_trackhub.html"> + <!-- Verify tracks folder contains bam and bai --> + <extra_files type="file" + name="myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb" + value="bed_simple_repeats/myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb" + compare="sim_size" + /> + </output> + </test> + + + <!-- Test with Psl --> + <test> + <param name="genome_name" value="Dbia3"/> + <param name="fasta_file" value="common/dbia3.fa"/> + <repeat name="group"> + <param name="group_name" value="Default group"/> + <repeat name="format"> + <conditional name="formatChoice"> + <param name="format_select" value="psl"/> + <param name="PSL" value="psl/inputs/blastXmlToPsl"/> + <param name="track_color" value="#000000"/> + </conditional> + </repeat> + </repeat> + <output name="output" file="psl/psl_trackhub.html"> + <!-- Verify tracks folder contains bam and bai --> + <extra_files type="file" + name="myHub/Dbia3/tracks/blastXmlToPsl.bb" + value="psl/myHub/Dbia3/tracks/blastXmlToPsl.bb" + compare="sim_size" + /> + <!-- Verify trackDb.txt contains the basic fields for a bam --> + <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition --> + </output> + </test> + + <!-- Test with BigWig --> + <test> + <param name="genome_name" value="Dbia3"/> + <param name="fasta_file" value="common/dbia3.fa"/> + <repeat name="group"> + <param name="group_name" value="Default group"/> + <repeat name="format"> + <conditional name="formatChoice"> + <param name="format_select" value="bigwig"/> + <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Summary"/> + <param name="track_color" value="#000000"/> + </conditional> + </repeat> + </repeat> + <output name="output" file="bigwig/bigwig.html"> + <!-- Verify tracks folder contains bam and bai --> + <extra_files type="file" + name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig" + value="bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig" + compare="sim_size" + /> + <!-- Verify trackDb.txt contains the basic fields for a bam --> + <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition --> + </output> + </test> + + <!-- Test with GFF3 --> + <test> + <param name="genome_name" value="Dbia3"/> + <param name="fasta_file" value="common/dbia3.fa"/> + <repeat name="group"> + <param name="group_name" value="Default group"/> + <repeat name="format"> + <conditional name="formatChoice"> + <param name="format_select" value="gff3"/> + <param name="GFF3" value="gff3/inputs/Augustus_Gene_Predictions"/> + <param name="track_color" value="#000000"/> + </conditional> + </repeat> + </repeat> + <output name="output" file="gff3/gff3_trackhub.html"> + <!-- Verify tracks folder contains bam and bai --> + <extra_files type="file" + name="myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb" + value="gff3/myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb" + compare="sim_size" + /> + <!-- Verify trackDb.txt contains the basic fields for a bam --> + <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition --> + </output> + </test> + + <!-- Test with GTF --> + <test> + <param name="genome_name" value="Dbia3"/> + <param name="fasta_file" value="common/dbia3.fa"/> + <repeat name="group"> + <param name="group_name" value="Default group"/> + <repeat name="format"> + <conditional name="formatChoice"> + <param name="format_select" value="gtf"/> + <param name="GTF" value="gtf/inputs/StringTie_Assembled_Transcripts"/> + <param name="track_color" value="#000000"/> + </conditional> + </repeat> + </repeat> + <output name="output" file="gtf/gtf_trackhub.html"> + <!-- Verify tracks folder contains bam and bai --> + <extra_files type="file" + name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb" + value="gtf/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb" + compare="sim_size" + /> + <!-- Verify trackDb.txt contains the basic fields for a bam --> + <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition --> + </output> + </test> + + <!-- Test with one group and multiple tracks --> + <test> + <param name="genome_name" value="Dbia3"/> + <param name="fasta_file" value="common/dbia3.fa"/> + <repeat name="group"> + <param name="group_name" value="Default group"/> + <repeat name="format"> + <conditional name="formatChoice"> + <param name="format_select" value="gtf"/> + <param name="GTF" value="gtf/inputs/StringTie_Assembled_Transcripts"/> + <param name="track_color" value="#000000"/> + </conditional> + </repeat> + <repeat name="format"> + <conditional name="formatChoice"> + <param name="format_select" value="gff3"/> + <param name="GFF3" value="gff3/inputs/Augustus_Gene_Predictions"/> + <param name="track_color" value="#000000"/> + </conditional> + </repeat> + </repeat> + <output name="output" file="gtf_gff/gtf_gff_trackhub.html"> + <!-- verify tracks folder contains bam and bai --> + <extra_files type="file" + name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb" + value="gtf/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb" + compare="sim_size" + /> + <extra_files type="file" + name="myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb" + value="gff3/myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb" + compare="sim_size" + /> + <!-- verify trackdb.txt contains the basic fields for a bam --> + <!-- todo: find a way to check also that the whole common structure is intact too, without too much repetition --> + </output> + </test> + + <!-- Test with one group and all the supported datatypes on 10/04/2016 --> + <test> + <param name="genome_name" value="Dbia3"/> + <param name="fasta_file" value="common/dbia3.fa"/> + <repeat name="group"> + <param name="group_name" value="Default group"/> + <repeat name="format"> + <conditional name="formatChoice"> + <param name="format_select" value="bam"/> + <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam"/> + <param name="track_color" value="#000000"/> + </conditional> + </repeat> + <repeat name="format"> + <conditional name="formatChoice"> + <param name="format_select" value="bed"/> + <conditional name="bedChoice"> + <param name="bed_select" value="bed_generic"/> + <param name="BED" ftype="bed" value="bed_generic/inputs/TBLASTN_Alignment_to_proteins"/> + <param name="track_color" value="#000000"/> + </conditional> + </conditional> + </repeat> + <repeat name="format"> + <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" ftype="bed" + value="bed_simple_repeats/inputs/Repeating_Elements_by_TrfBig"/> + <param name="track_color" value="#000000"/> + </conditional> + </conditional> + </repeat> + <repeat name="format"> + <conditional name="formatChoice"> + <param name="format_select" value="psl"/> + <param name="PSL" value="psl/inputs/blastXmlToPsl"/> + <param name="track_color" value="#000000"/> + </conditional> + </repeat> + <repeat name="format"> + <conditional name="formatChoice"> + <param name="format_select" value="bigwig"/> + <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Summary"/> + <param name="track_color" value="#000000"/> + </conditional> + </repeat> + <repeat name="format"> + <conditional name="formatChoice"> + <param name="format_select" value="gff3"/> + <param name="GFF3" value="gff3/inputs/Augustus_Gene_Predictions"/> + <param name="track_color" value="#000000"/> + </conditional> + </repeat> + <repeat name="format"> + <conditional name="formatChoice"> + <param name="format_select" value="gtf"/> + <param name="GTF" value="gtf/inputs/StringTie_Assembled_Transcripts"/> + <param name="track_color" value="#000000"/> + </conditional> + </repeat> + </repeat> + <output name="output" file="all_datatypes/all_datatypes_trackhub.html"> + <!-- verify tracks folder contains all the files --> + <extra_files type="file" + name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam" + value="all_datatypes/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam" + compare="sim_size" + /> + <extra_files type="file" + name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai" + value="all_datatypes/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai" + compare="sim_size" + /> + <extra_files type="file" + name="myHub/Dbia3/tracks/TBLASTN_Alignment_to_proteins.bb" + value="all_datatypes/myHub/Dbia3/tracks/TBLASTN_Alignment_to_proteins.bb" + compare="sim_size" + /> + <extra_files type="file" + name="myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb" + value="all_datatypes/myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb" + compare="sim_size" + /> + <extra_files type="file" + name="myHub/Dbia3/tracks/blastXmlToPsl.bb" + value="all_datatypes/myHub/Dbia3/tracks/blastXmlToPsl.bb" + compare="sim_size" + /> + <extra_files type="file" + name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig" + value="all_datatypes/myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig" + compare="sim_size" + /> + <extra_files type="file" + name="myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb" + value="all_datatypes/myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb" + compare="sim_size" + /> + <extra_files type="file" + name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb" + value="all_datatypes/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb" + compare="sim_size" + /> + <!-- verify trackdb.txt contains the basic fields for a bam --> + <!-- todo: find a way to check also that the whole common structure is intact too, without too much repetition --> + </output> + </test> + + <!-- Test with two groups and no tracks --> + <test> + <param name="genome_name" value="Dbia3"/> + <param name="fasta_file" value="common/dbia3.fa"/> + <repeat name="group"> + <param name="group_name" value="Default group"/> + </repeat> + <repeat name="group"> + <param name="group_name" value="Other group"/> + </repeat> + <output name="output" file="two_groups_no_track/two_groups_no_track_trackhub.html"> + <extra_files type="file" name="myHub/genomes.txt" value="two_groups_no_track/myHub/genomes.txt"/> + <extra_files type="file" name="myHub/Dbia3.html" value="two_groups_no_track/myHub/Dbia3.html"/> + <!-- Email could be different, but we need to ensure we still have the email line --> + <extra_files type="file" name="myHub/hub.txt" value="two_groups_no_track/myHub/hub.txt" lines_diff="2"> + <assert_contents> + <has_text text="email"/> + </assert_contents> + </extra_files> + <extra_files type="file" name="myHub/Dbia3/Dbia3.2bit" value="common/Dbia3.2bit"> + </extra_files> + <extra_files type="file" name="myHub/Dbia3/description.html" + value="two_groups_no_track/myHub/Dbia3/description.html"/> + </output> + </test> + + <!-- Test with two groups and one track in first --> + <test> + <param name="genome_name" value="Dbia3"/> + <param name="fasta_file" value="common/dbia3.fa"/> + <repeat name="group"> + <param name="group_name" value="Default group"/> + <repeat name="format"> + <conditional name="formatChoice"> + <param name="format_select" value="bigwig"/> + <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Summary"/> + <param name="track_color" value="#000000"/> + </conditional> + </repeat> + </repeat> + <repeat name="group"> + <param name="group_name" value="Other group"/> + </repeat> + <output name="output" file="two_groups_one_track_first/two_groups_one_track_first_trackhub.html"> + <!-- Check myHub structure --> + <extra_files type="file" name="myHub/genomes.txt" value="two_groups_one_track_first/myHub/genomes.txt"/> + <extra_files type="file" name="myHub/Dbia3.html" value="two_groups_one_track_first/myHub/Dbia3.html"/> + <!-- Email could be different, but we need to ensure we still have the email line --> + <extra_files type="file" name="myHub/hub.txt" value="two_groups_one_track_first/myHub/hub.txt" lines_diff="2"> + <assert_contents> + <has_text text="email"/> + </assert_contents> + </extra_files> + <extra_files type="file" name="myHub/Dbia3/Dbia3.2bit" value="common/Dbia3.2bit"> + </extra_files> + <extra_files type="file" name="myHub/Dbia3/description.html" + value="two_groups_one_track_first/myHub/Dbia3/description.html"/> + + <!-- Check tracks exist --> + <extra_files type="file" + name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig" + value="bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig" + compare="sim_size" + /> + + <!-- Check the groups.txt exists and is properly populated --> + </output> + </test> + + <!-- Test with two groups and one track in both --> + <test> + <param name="genome_name" value="Dbia3"/> + <param name="fasta_file" value="common/dbia3.fa"/> + <repeat name="group"> + <param name="group_name" value="Default group"/> + <repeat name="format"> + <conditional name="formatChoice"> + <param name="format_select" value="bigwig"/> + <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Summary"/> + <param name="track_color" value="#000000"/> + </conditional> + </repeat> + </repeat> + <repeat name="group"> + <param name="group_name" value="Other group"/> + <repeat name="format"> + <conditional name="formatChoice"> + <param name="format_select" value="gtf"/> + <param name="GTF" value="gtf/inputs/StringTie_Assembled_Transcripts"/> + <param name="track_color" value="#000000"/> + </conditional> + </repeat> + </repeat> + <output name="output" file="two_groups_one_track_both/two_groups_one_track_both_trackhub.html"> + <!-- Check myHub structure --> + <extra_files type="file" name="myHub/genomes.txt" value="two_groups_one_track_both/myHub/genomes.txt"/> + <extra_files type="file" name="myHub/Dbia3.html" value="two_groups_one_track_both/myHub/Dbia3.html"/> + <!-- Email could be different, but we need to ensure we still have the email line --> + <extra_files type="file" name="myHub/hub.txt" value="two_groups_one_track_both/myHub/hub.txt" + lines_diff="2"> + <assert_contents> + <has_text text="email"/> + </assert_contents> + </extra_files> + <extra_files type="file" name="myHub/Dbia3/Dbia3.2bit" value="common/Dbia3.2bit"> + </extra_files> + <extra_files type="file" name="myHub/Dbia3/description.html" + value="two_groups_one_track_both/myHub/Dbia3/description.html"/> + + <!-- Check tracks exist --> + <!-- First group --> + <extra_files type="file" + name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig" + value="bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig" + compare="sim_size" + /> + + <!-- Second group --> + <extra_files type="file" + name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb" + value="gtf/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb" + compare="sim_size" + /> + <!-- Check the groups.txt exists and is properly populated --> + </output> + </test> + + <!-- Test with two groups and multiple tracks in both --> + <test> + <param name="genome_name" value="Dbia3"/> + <param name="fasta_file" value="common/dbia3.fa"/> + <repeat name="group"> + <param name="group_name" value="Default group"/> + <repeat name="format"> + <conditional name="formatChoice"> + <param name="format_select" value="bigwig"/> + <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Summary"/> + <param name="track_color" value="#000000"/> + </conditional> + </repeat> + <repeat name="format"> + <conditional name="formatChoice"> + <param name="format_select" value="bam"/> + <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam"/> + <param name="track_color" value="#000000"/> + </conditional> + </repeat> + </repeat> + <repeat name="group"> + <param name="group_name" value="Other group"/> + <repeat name="format"> + <conditional name="formatChoice"> + <param name="format_select" value="gtf"/> + <param name="GTF" value="gtf/inputs/StringTie_Assembled_Transcripts"/> + <param name="track_color" value="#000000"/> + </conditional> + </repeat> + <repeat name="format"> + <conditional name="formatChoice"> + <param name="format_select" value="gff3"/> + <param name="GFF3" value="gff3_multi_fasta/inputs/Multi-Fasta_GlimmerHMM_Gene_Predictions"/> + <param name="track_color" value="#000000"/> + </conditional> + </repeat> + </repeat> + <output name="output" file="two_groups_multiple_tracks/two_groups_multiple_tracks_trackhub.html"> + <!-- Check myHub structure --> + <extra_files type="file" name="myHub/genomes.txt" value="two_groups_multiple_tracks/myHub/genomes.txt"/> + <extra_files type="file" name="myHub/Dbia3.html" value="two_groups_multiple_tracks/myHub/Dbia3.html"/> + <!-- Email could be different, but we need to ensure we still have the email line --> + <extra_files type="file" name="myHub/hub.txt" value="two_groups_multiple_tracks/myHub/hub.txt" + lines_diff="2"> + <assert_contents> + <has_text text="email"/> + </assert_contents> + </extra_files> + <extra_files type="file" name="myHub/Dbia3/Dbia3.2bit" value="common/Dbia3.2bit"> + </extra_files> + <extra_files type="file" name="myHub/Dbia3/description.html" + value="two_groups_multiple_tracks/myHub/Dbia3/description.html"/> + + <!-- Check tracks exist --> + <!-- First group --> + <extra_files type="file" + name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig" + value="bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig" + compare="sim_size" + /> + <extra_files type="file" + name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam" + value="bam/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam" + compare="sim_size" + /> + <extra_files type="file" + name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai" + value="bam/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai" + compare="sim_size" + /> + + <!-- Second group --> + <extra_files type="file" + name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb" + value="gtf/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb" + compare="sim_size" + /> + <extra_files type="file" + name="myHub/Dbia3/tracks/Multi-Fasta_GlimmerHMM_Gene_Predictions.bb" + value="gff3_multi_fasta/myHub/Dbia3/tracks/Multi-Fasta_GlimmerHMM_Gene_Predictions.bb" + compare="sim_size" + /> + <!-- Check the groups.txt exists and is properly populated --> + </output> + </test> + + <!-- Test default color in a track --> + <test> + <param name="genome_name" value="Dbia3"/> + <param name="fasta_file" value="common/dbia3.fa"/> + <repeat name="group"> + <param name="group_name" value="Default group"/> + <repeat name="format"> + <conditional name="formatChoice"> + <param name="format_select" value="bam"/> + <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam"/> + <param name="track_color" value="#000000"/> + </conditional> + </repeat> + </repeat> + <output name="output" file="default_color/default_color_trackhub.html"> + <!-- Verify trackDb.txt contains the color 0,0,0 --> + <extra_files type="file" name="myHub/Dbia3/trackDb.txt" value="default_color/myHub/Dbia3/trackDb.txt"> + <assert_contents> + <has_text text="color 0,0,0"/> + </assert_contents> + </extra_files> + + <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition --> + </output> + </test> + + <!-- Test changed color in a track --> + <test> + <param name="genome_name" value="Dbia3"/> + <param name="fasta_file" value="common/dbia3.fa"/> + <repeat name="group"> + <param name="group_name" value="Default group"/> + <repeat name="format"> + <conditional name="formatChoice"> + <param name="format_select" value="bam"/> + <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam"/> + <param name="track_color" value="#8064a2"/> + </conditional> + </repeat> + </repeat> + <output name="output" file="changed_color/changed_color_trackhub.html"> + <!-- Verify trackDb.txt contains the color 128,100,162 --> + <extra_files type="file" name="myHub/Dbia3/trackDb.txt" value="changed_color/myHub/Dbia3/trackDb.txt"> + <assert_contents> + <has_text text="color 128,100,162"/> + </assert_contents> + </extra_files> + + <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition --> + </output> + </test> + + <!-- Test for StringTie Chromosome end coordinates --> + <test> + <param name="genome_name" value="Dbia3"/> + <param name="fasta_file" value="common/dbia3.fa"/> + <repeat name="group"> + <param name="group_name" value="Default group"/> + <repeat name="format"> + <conditional name="formatChoice"> + <param name="format_select" value="gtf"/> + <param name="GTF" ftype="gtf" value="stringtie_chromosome_end_coordinates/inputs/StringTie_Assembled_Transcripts"/> + <param name="track_color" value="#000000"/> + </conditional> + </repeat> + </repeat> + <output name="output" file="stringtie_chromosome_end_coordinates/stringtie_chromosome_end_coordinates_trackhub.html"> + <extra_files type="file" + name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb" + value="stringtie_chromosome_end_coordinates/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb" + compare="sim_size" + /> + + <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition --> + </output> + </test> + + <!-- Test for big files? --> + + <!-- Find tests that should fail --> + + </tests> + + <help> + This Galaxy tool permits to prepare your files to be ready for + Assembly Hub visualization. + </help> +</tool>