Mercurial > repos > rmarenco > hubarchivecreator
view hubArchiveCreator.xml @ 31:9c5d82d3c87e draft
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit cd459f55fcb828e250986412fb779234ad89b3b2
| author | yating-l |
|---|---|
| date | Tue, 19 Jun 2018 13:16:08 -0400 |
| parents | e7c4be523cb7 |
| children | 6d1f2bb5c1d1 |
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<tool id="hubArchiveCreator" name="Hub Archive Creator" version="2.5.2"> <description> This Galaxy tool permits to prepare your files to be ready for Assembly Hub visualization. </description> <macros> <import>macros.xml</import> </macros> <requirements> <requirement type="package" version="340">ucsc_hac</requirement> <requirement type="package" version="1.2">samtools</requirement> <requirement type="package" version="340">ucsc_bigwig</requirement> <requirement type="package" version="340">ucsc_bigbed</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; ## Dump the tool parameters into a JSON file python $json_file parameters.json; python $__tool_directory__/hubArchiveCreator.py --data_json parameters.json -o $output; ]]></command> <configfiles> <configfile name="json_file"> import json import sys file_path = sys.argv[1] #set global $data_parameter_dict = {} ## Ask the user to enter the genome name #silent $data_parameter_dict.update({"genome_name": str($genome_name)}) ## Function to retrieve the data of the inputs #def prepare_json($datatype, $input_to_prepare, $order_index, $extra_data_dict={}) #set false_path = str($input_to_prepare) #set $data_dict = {"false_path": $false_path} #set name = str($input_to_prepare.name) #silent $data_dict.update({"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}) #if $datatype in $data_parameter_dict #silent $data_parameter_dict[$datatype].append($data_dict) #else #set array_inputs = [] #silent $array_inputs.append($data_dict) #silent $data_parameter_dict.update({$datatype: $array_inputs}) #end if #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($g.group_name) #set longLabel = str($f.formatChoice.longLabel) #set extra_data_dict = {"track_color": $track_color, "group_name": $group_name, "long_label": $longLabel} #if $f.formatChoice.format_select == "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("Bam", $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" #silent $prepare_json("Bed", $f.formatChoice.bedChoice.BED, $index_track_final, $extra_data_dict) #end if #if $f.formatChoice.bedChoice.bed_select == "bed_cytoBand" #silent $prepare_json("CytoBand", $f.formatChoice.bedChoice.BED_cytoBand, $index_track_final, $extra_data_dict) #end if #if $f.formatChoice.bedChoice.bed_select == "bed_simple_repeats_option" #silent $prepare_json("BedSimpleRepeats", $f.formatChoice.bedChoice.BED_simple_repeats, $index_track_final, $extra_data_dict) #end if #if $f.formatChoice.bedChoice.bed_select == "bed_splice_junctions_option" #silent $prepare_json("BedSpliceJunctions", $f.formatChoice.bedChoice.BED_splice_junctions, $index_track_final, $extra_data_dict) #end if #if $f.formatChoice.bedChoice.bed_select == "bed_blast_alignment_option" #set database = str($f.formatChoice.bedChoice.database) #silent $extra_data_dict.update({"database": $database}) #if $f.formatChoice.bedChoice.add_trix_index.add_trix_index_selector == "yes" #for i in $f.formatChoice.bedChoice.add_trix_index.trix_index #if $i.element_identifier.endswith("ix") #$extra_data_dict.update({"index_ix": str($i)}) #elif $i.element_identifier.endswith("ixx") #$extra_data_dict.update({"index_ixx": str($i)}) #end if #end for ##set ix_index = str($f.formatChoice.bedChoice.add_trix_index.trix_index.index_ix) ##set ixx_index = str($f.formatChoice.bedChoice.add_trix_index.trix_index.index_ixx) ##silent $extra_data_dict.update({"indexIx": $ix_index, "indexIxx": $ixx_index}) #end if #silent $prepare_json("BedBlastAlignments", $f.formatChoice.bedChoice.BED_blast_alignment, $index_track_final, $extra_data_dict) #end if #if $f.formatChoice.bedChoice.bed_select == "bed_blat_alignment_option" #set database = str($f.formatChoice.bedChoice.database) #silent $extra_data_dict.update({"database": $database}) #if $f.formatChoice.bedChoice.add_trix_index.add_trix_index_selector == "yes" #for i in $f.formatChoice.bedChoice.add_trix_index.trix_index #if $i.element_identifier.endswith("ix") #$extra_data_dict.update({"index_ix": str($i)}) #elif $i.element_identifier.endswith("ixx") #$extra_data_dict.update({"index_ixx": str($i)}) #end if #end for ##set ix_index = str($f.formatChoice.bedChoice.add_trix_index.trix_index.index_ix) ##set ixx_index = str($f.formatChoice.bedChoice.add_trix_index.trix_index.index_ixx) ##silent $extra_data_dict.update({"indexIx": $ix_index, "indexIxx": $ixx_index}) #end if #silent $prepare_json("BedBlatAlignments", $f.formatChoice.bedChoice.BED_blat_alignment, $index_track_final, $extra_data_dict) #end if #end if #if $f.formatChoice.format_select == "psl" #silent $prepare_json("Psl", $f.formatChoice.PSL, $index_track_final, $extra_data_dict) #end if #if $f.formatChoice.format_select == "bigwig" #silent $prepare_json("BigWig", $f.formatChoice.BIGWIG, $index_track_final, $extra_data_dict) #end if #if $f.formatChoice.format_select == "bigbed" #if $f.formatChoice.add_trix_index.add_trix_index_selector == "yes" ##set ix_index = str($f.formatChoice.add_trix_index.trix_index.index_ix) ##set ixx_index = str($f.formatChoice.add_trix_index.trix_index.index_ixx) #for i in $f.formatChoice.add_trix_index.trix_index #if $i.element_identifier.endswith("ix") #$extra_data_dict.update({"index_ix": str($i)}) #elif $i.element_identifier.endswith("ixx") #$extra_data_dict.update({"index_ixx": str($i)}) #end if #end for #$extra_data_dict.update({"trix_id": str($f.formatChoice.add_trix_index.trix_id)}) ##set trix_id = str($f.formatChoice.add_trix_index.trix_id) ##silent $extra_data_dict.update({"indexIx": $ix_index, "indexIxx": $ixx_index, "trix_id": $trix_id}) #end if #silent $prepare_json("BigBed", $f.formatChoice.BIGBED, $index_track_final, $extra_data_dict) #end if #if $f.formatChoice.format_select == "gff3" #silent $prepare_json("Gff3", $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 #silent $prepare_json("Gtf", $f.formatChoice.GTF, $index_track_final, $extra_data_dict) #end if #end for #end for ## We combine the fasta file dataset name with his false path in a JSON object #set fasta_json = {"false_path": str($fasta_file), "name": str($fasta_file.name)} $data_parameter_dict.update({"fasta": $fasta_json}) ## Retrieve the user email #silent $data_parameter_dict.update({"user_email": str($__user_email__)}) #silent $data_parameter_dict.update({"tool_directory": str($__tool_directory__)}) #silent $data_parameter_dict.update({"extra_files_path": str($output.extra_files_path)}) #silent $data_parameter_dict.update({"debug_mode": str($advanced_options.debug_mode)}) with open(file_path, 'w') as f: json.dump($data_parameter_dict, f) </configfile> </configfiles> <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="bigbed">BIGBED</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="longLabel" type="text" size="76" label="Track label" help="It is limited to 76 printable characters, the first 17 printable characters will be used as a short label of the track" /> <!-- 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</option> <option value="bed_cytoBand">cytoBand Track (bed4+1)</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> <option value="bed_blast_alignment_option">Blast alignments (bed12+12 / bigPsl.as)</option> <option value="bed_blat_alignment_option">BLAT alignments (bigPsl / bigPsl.as)</option> </param> <when value="bed_generic"> <param format="bed" name="BED" type="data" label="Generic Bed File Choice" /> </when> <when value="bed_cytoBand"> <param format="bed" name="BED_cytoBand" type="data" label="cytoBand Track (Bed4)" /> </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> <when value="bed_blast_alignment_option"> <param format="bed" name="BED_blast_alignment" type="data" label="Bed Blast Alignments (Bed12+12) File" /> <param name="database" type="select" label="Protein database"> <option value="NCBI" selected="true">NCBI</option> <option value="UniProt">UniProt</option> <option value="FlyBase">FlyBase</option> <option value="Others">Others</option> </param> <expand macro="add_trix_file"/> </when> <when value="bed_blat_alignment_option"> <param format="bed" name="BED_blat_alignment" type="data" label="Bed BLAT Alignments (bigPsl) File" /> <param name="database" type="select" label="mRNA database"> <option value="NCBI" selected="true">NCBI</option> <option value="Others">Others</option> </param> <expand macro="add_trix_file"/> </when> </conditional> <param name="longLabel" type="text" size="76" label="Track label" help="It is limited to 76 printable characters, the first 17 printable characters will be used as a short label of the track" /> <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="longLabel" type="text" size="76" label="Track label" help="It is limited to 76 printable characters, the first 17 printable characters will be used as a short label of the track" /> <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="longLabel" type="text" size="76" label="Track label" help="It is limited to 76 printable characters, the first 17 printable characters will be used as a short label of the track" /> <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="bigbed"> <param format="bigbed" name="BIGBED" type="data" label="BIGBED File" /> <expand macro="add_trix_file"> <param name="trix_id" value="name" type="text" size="30" label="Specify Trix identifier (The default is name)" /> </expand> <param name="longLabel" type="text" size="76" label="Track label" help="It is limited to 76 printable characters, the first 17 printable characters will be used as a short label of the track" /> <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="longLabel" type="text" size="76" label="Track label" help="It is limited to 76 printable characters, the first 17 printable characters will be used as a short label of the track" /> <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="longLabel" type="text" size="76" label="Track label" help="It is limited to 76 printable characters, the first 17 printable characters will be used as a short label of the track" /> <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="select" label="Activate debug mode"> <option value="false" selected="true">No</option> <option value="true">Yes</option> <help> Use this option if you are a G-OnRamp developer </help> </param> </when> <when value="off"> <param name="debug_mode" type="hidden" value="false"> </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"> <!-- Use macro to check the whole common structure without repeated code --> <expand macro="verify_hub_structure_no_track" test="only_genome" /> </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="longLabel" value="HISAT sequence alignment" /> <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" /> <!-- Use macro to check the whole common structure without repeated code --> <expand macro="verify_hub_structure" test="bam" /> </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="longLabel" value="TBLASTN alignment" /> <param name="track_color" value="#000000"/> </conditional> </conditional> </repeat> </repeat> <output name="output" file="bed_generic/bed_generic.html"> <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" /> <expand macro="verify_hub_structure" test="bed_generic" /> </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="longLabel" value="Simple repeat" /> <param name="track_color" value="#000000"/> </conditional> </conditional> </repeat> </repeat> <output name="output" file="bed_simple_repeats/bed_simple_repeats_trackhub.html"> <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" /> <expand macro="verify_hub_structure" test="bed_simple_repeats" /> </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="longLabel" value="BLAST Alignment" /> <param name="track_color" value="#000000"/> </conditional> </repeat> </repeat> <output name="output" file="psl/psl_trackhub.html"> <extra_files type="file" name="myHub/Dbia3/tracks/blastXmlToPsl.bb" value="psl/myHub/Dbia3/tracks/blastXmlToPsl.bb" compare="sim_size" /> <expand macro="verify_hub_structure" test="psl" /> </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_Coverage"/> <param name="longLabel" value="RNA-Seq Coverage" /> <param name="track_color" value="#000000"/> </conditional> </repeat> </repeat> <output name="output" file="bigwig/bigwig.html"> <extra_files type="file" name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig" value="bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig" compare="sim_size" /> <expand macro="verify_hub_structure" test="bigwig" /> <!-- check additional trackDb settings for BigWig --> <extra_files type="file" name="myHub/Dbia3/trackDb.txt"> <assert_contents> <has_text text="autoScale"/> <has_text text="maxHeightPixels"/> <has_text text="windowingFunction"/> </assert_contents> </extra_files> </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="longLabel" value="Augustus" /> <param name="track_color" value="#000000"/> </conditional> </repeat> </repeat> <output name="output" file="gff3/gff3_trackhub.html"> <extra_files type="file" name="myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb" value="gff3/myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb" compare="sim_size" /> <expand macro="verify_hub_structure" test="gff3" /> </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="longLabel" value="StringTie transcripts" /> <param name="track_color" value="#000000"/> </conditional> </repeat> </repeat> <output name="output" file="gtf/gtf_trackhub.html"> <extra_files type="file" name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb" value="gtf/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb" compare="sim_size" /> <expand macro="verify_hub_structure" test="gtf" /> </output> </test> <!-- Test with BLAT Alignment --> <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_blat_alignment_option"/> <param name="BED_blat_alignment" ftype="bed" value="bed_blat_alignment/inputs/BLAT_alignment_bigpsl"/> <param name="longLabel" value="BLAT alignment" /> <param name="track_color" value="#000000"/> <param name="database" value="NCBI" /> </conditional> </conditional> </repeat> </repeat> <output name="output" file="bed_blat_alignment/blat_alignment_trackhub.html"> <extra_files type="file" name="myHub/Dbia3/tracks/BLAT_alignment_bigpsl.bb" value="bed_blat_alignment/myHub/Dbia3/tracks/BLAT_alignment_bigpsl.bb" compare="sim_size" /> <expand macro="verify_hub_structure" test="bed_blat_alignment" /> <!-- check additional trackDb settings for BLAT --> <extra_files type="file" name="myHub/Dbia3/trackDb.txt"> <assert_contents> <has_text text="searchIndex"/> <has_text text="url"/> <has_text text="urlLabel"/> <has_text text="iframeUrl"/> <has_text text="iframeOptions"/> </assert_contents> </extra_files> </output> </test> <!-- Test with BLAST Alignment --> <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_blast_alignment_option"/> <param name="BED_blast_alignment" ftype="bed" value="bed_blast_alignment/inputs/BLAST_alignment_bigpsl"/> <param name="longLabel" value="BLAST alignment" /> <param name="track_color" value="#000000"/> <param name="database" value="NCBI" /> </conditional> </conditional> </repeat> </repeat> <output name="output" file="bed_blast_alignment/blast_alignment_trackhub.html"> <extra_files type="file" name="myHub/Dbia3/tracks/BLAST_alignment_bigpsl.bb" value="bed_blast_alignment/myHub/Dbia3/tracks/BLAST_alignment_bigpsl.bb" compare="sim_size" /> <expand macro="verify_hub_structure" test="bed_blast_alignment" /> <!-- check additional trackDb settings for BLAST --> <extra_files type="file" name="myHub/Dbia3/trackDb.txt"> <assert_contents> <has_text text="searchIndex"/> <has_text text="url"/> <has_text text="urlLabel"/> <has_text text="iframeUrl"/> <has_text text="iframeOptions"/> </assert_contents> </extra_files> </output> </test> <!-- Test with Regtools Splice Junctions --> <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_splice_junctions_option"/> <param name="BED_splice_junctions" ftype="bed" value="bed_splice_junctions/inputs/regtools_junctions"/> <param name="longLabel" value="Splice junctions" /> <param name="track_color" value="#000000"/> </conditional> </conditional> </repeat> </repeat> <output name="output" file="bed_splice_junctions/splice_junctions_trackhub.html"> <extra_files type="file" name="myHub/Dbia3/tracks/regtools_junctions.bb" value="bed_splice_junctions/myHub/Dbia3/tracks/regtools_junctions.bb" compare="sim_size" /> <expand macro="verify_hub_structure" test="bed_splice_junctions" /> </output> </test> <!-- Test with Cytoband --> <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_cytoBand"/> <param name="BED_cytoBand" ftype="bed" value="bed_cytoband/inputs/Cytoband"/> <param name="longLabel" value="Cytoband" /> <param name="track_color" value="#000000"/> </conditional> </conditional> </repeat> </repeat> <output name="output" file="bed_cytoband/cytoband_trackhub.html"> <extra_files type="file" name="myHub/Dbia3/tracks/Cytoband.bb" value="bed_cytoband/myHub/Dbia3/tracks/Cytoband.bb" compare="sim_size" /> <expand macro="verify_hub_structure" test="bed_cytoband" /> <extra_files type="file" name="myHub/Dbia3/trackDb.txt"> <assert_contents> <has_text text="track cytoBandIdeo"/> </assert_contents> </extra_files> </output> </test> <!-- Test with bigBed --> <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="bigbed"/> <param name="BIGBED" value="big_bed/inputs/BLAT_alignment_bigbed" /> <param name="longLabel" value="bigBed" /> <param name="track_color" value="#000000"/> </conditional> </repeat> </repeat> <output name="output" file="big_bed/bigbed_trackhub.html"> <extra_files type="file" name="myHub/Dbia3/tracks/BLAT_alignment_bigbed.bigbed" value="big_bed/myHub/Dbia3/tracks/BLAT_alignment_bigbed.bigbed" compare="sim_size" /> <expand macro="verify_hub_structure" test="big_bed" /> </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"> <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" /> <expand macro="verify_hub_structure" test="gtf_gff" /> </output> </test> <!-- Test with one group and all the supported datatypes --> <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_Coverage"/> <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 name="format"> <conditional name="formatChoice"> <param name="format_select" value="bed" /> <conditional name="bedChoice"> <param name="bed_select" value="bed_cytoBand"/> <param name="BED_cytoBand" ftype="bed" value="bed_cytoband/inputs/Cytoband"/> <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_splice_junctions_option"/> <param name="BED_splice_junctions" ftype="bed" value="bed_splice_junctions/inputs/regtools_junctions"/> <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_blast_alignment_option"/> <param name="BED_blast_alignment" ftype="bed" value="bed_blast_alignment/inputs/BLAST_alignment_bigpsl"/> <param name="track_color" value="#000000"/> <param name="database" value="NCBI" /> </conditional> </conditional> </repeat> <repeat name="format"> <conditional name="formatChoice"> <param name="format_select" value="bed" /> <conditional name="bedChoice"> <param name="bed_select" value="bed_blat_alignment_option"/> <param name="BED_blat_alignment" ftype="bed" value="bed_blat_alignment/inputs/BLAT_alignment_bigpsl"/> <param name="track_color" value="#000000"/> <param name="database" value="NCBI" /> </conditional> </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_Coverage.bigwig" value="all_datatypes/myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.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" /> <extra_files type="file" name="myHub/Dbia3/tracks/Cytoband.bb" value="all_datatypes/myHub/Dbia3/tracks/Cytoband.bb" compare="sim_size" /> <extra_files type="file" name="myHub/Dbia3/tracks/regtools_junctions.bb" value="all_datatypes/myHub/Dbia3/tracks/regtools_junctions.bb" compare="sim_size" /> <extra_files type="file" name="myHub/Dbia3/tracks/BLAST_alignment_bigpsl.bb" value="all_datatypes/myHub/Dbia3/tracks/BLAST_alignment_bigpsl.bb" compare="sim_size" /> <extra_files type="file" name="myHub/Dbia3/tracks/BLAT_alignment_bigpsl.bb" value="all_datatypes/myHub/Dbia3/tracks/BLAT_alignment_bigpsl.bb" compare="sim_size" /> <expand macro="verify_hub_structure" test="all_datatypes" /> </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"> <expand macro="verify_hub_structure_no_track" test="two_groups_no_track" /> </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_Coverage"/> <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 tracks exist --> <extra_files type="file" name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig" value="bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig" compare="sim_size" /> <expand macro="verify_hub_structure" test="two_groups_one_track_first" /> </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_Coverage"/> <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 tracks exist --> <!-- First group --> <extra_files type="file" name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig" value="bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.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" /> <expand macro="verify_hub_structure" test="two_groups_one_track_both" /> <!-- 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_Coverage"/> <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 tracks exist --> <!-- First group --> <extra_files type="file" name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig" value="bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.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" /> <expand macro="verify_hub_structure" test="two_groups_multiple_tracks" /> </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"> <expand macro="verify_hub_structure" test="default_color" /> <!-- Verify trackDb.txt contains the color 0,0,0 --> <extra_files type="file" name="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"> <expand macro="verify_hub_structure" test="changed_color" /> <!-- Verify trackDb.txt contains the color 128,100,162 --> <extra_files type="file" name="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" /> <expand macro="verify_hub_structure" test="stringtie_chromosome_end_coordinates" /> <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition --> </output> </test> <!-- Test default label 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"> <expand macro="verify_hub_structure" test="default_color" /> <!-- Verify trackDb.txt contains default label --> <extra_files type="file" name="myHub/Dbia3/trackDb.txt"> <assert_contents> <has_text text="longLabel HISAT2 Accepted Hits.bam"/> </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 customized label 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="longLabel" value="HISAT sequence alignment" /> <param name="track_color" value="#000000"/> </conditional> </repeat> </repeat> <output name="output" file="changed_label/changed_label_trackhub.html"> <expand macro="verify_hub_structure" test="changed_label" /> <!-- Verify trackDb.txt contains the customized label --> <extra_files type="file" name="myHub/Dbia3/trackDb.txt"> <assert_contents> <has_text text="longLabel HISAT sequence alignment"/> </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 TrixIndex for Blat alignment 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="bed" /> <conditional name="bedChoice"> <param name="bed_select" value="bed_blat_alignment_option"/> <param name="BED_blat_alignment" ftype="bed" value="bed_blat_alignment/inputs/BLAT_alignment_bigpsl"/> <param name="longLabel" value="BLAT alignment" /> <param name="track_color" value="#000000"/> <param name="database" value="NCBI" /> <conditional name="add_trix_index"> <param name="add_trix_index_selector" value="yes" /> <param name="trix_index" value="trix_index_files/blat_out.ix,trix_index_files/blat_out.ixx" /> </conditional> </conditional> </conditional> </repeat> </repeat> <param name="debug_mode" value="true" /> <output name="output" file="trix_index_files/blat_alignment_trackhub.html"> <extra_files type="file" name="myHub/Dbia3/tracks/BLAT_alignment_bigpsl.bb" value="bed_blat_alignment/myHub/Dbia3/tracks/BLAT_alignment_bigpsl.bb" compare="sim_size" /> <expand macro="verify_hub_structure" test="bed_blat_alignment" /> <!-- check additional trackDb settings for BLAT --> <extra_files type="file" name="myHub/Dbia3/trackDb.txt"> <assert_contents> <has_text text="searchIndex"/> <has_text text="searchTrix"/> <has_text text="url"/> <has_text text="urlLabel"/> <has_text text="iframeUrl"/> <has_text text="iframeOptions"/> </assert_contents> </extra_files> <!-- check Trix index directory --> <extra_files type="file" name="myHub/Dbia3/trix/BLAT_alignment_bigpsl.bb.ix" value="trix_index_files/blat_out.ix" /> <extra_files type="file" name="myHub/Dbia3/trix/BLAT_alignment_bigpsl.bb.ixx" value="trix_index_files/blat_out.ixx" /> </output> </test> <!-- Test TrixIndex for BLAST Alignment --> <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_blast_alignment_option"/> <param name="BED_blast_alignment" ftype="bed" value="bed_blast_alignment/inputs/BLAST_alignment_bigpsl"/> <param name="longLabel" value="BLAST alignment" /> <param name="track_color" value="#000000"/> <param name="database" value="NCBI" /> <conditional name="add_trix_index"> <param name="add_trix_index_selector" value="yes" /> <param name="trix_index" value="trix_index_files/blast_out.ix,trix_index_files/blast_out.ixx" /> </conditional> </conditional> </conditional> </repeat> </repeat> <param name="debug_mode" value="true" /> <output name="output" file="trix_index_files/blast_alignment_trackhub.html"> <extra_files type="file" name="myHub/Dbia3/tracks/BLAST_alignment_bigpsl.bb" value="bed_blast_alignment/myHub/Dbia3/tracks/BLAST_alignment_bigpsl.bb" compare="sim_size" /> <expand macro="verify_hub_structure" test="bed_blast_alignment" /> <!-- check additional trackDb settings for BLAST --> <extra_files type="file" name="myHub/Dbia3/trackDb.txt"> <assert_contents> <has_text text="searchIndex"/> <has_text text="searchTrix"/> <has_text text="url"/> <has_text text="urlLabel"/> <has_text text="iframeUrl"/> <has_text text="iframeOptions"/> </assert_contents> </extra_files> <!-- check Trix index directory --> <extra_files type="file" name="myHub/Dbia3/trix/BLAST_alignment_bigpsl.bb.ix" value="trix_index_files/blast_out.ix" /> <extra_files type="file" name="myHub/Dbia3/trix/BLAST_alignment_bigpsl.bb.ixx" value="trix_index_files/blast_out.ixx" /> </output> </test> <!-- Test TrixIndex for BigBed --> <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="bigbed"/> <param name="BIGBED" value="big_bed/inputs/BLAT_alignment_bigbed" /> <param name="longLabel" value="bigBed" /> <param name="track_color" value="#000000"/> <conditional name="add_trix_index"> <param name="add_trix_index_selector" value="yes" /> <param name="trix_index" value="trix_index_files/blat_out.ix,trix_index_files/blat_out.ixx" /> <param name="trix_id" value="name" /> </conditional> </conditional> </repeat> </repeat> <param name="debug_mode" value="true" /> <output name="output" file="trix_index_files/bigbed_trackhub.html"> <extra_files type="file" name="myHub/Dbia3/tracks/BLAT_alignment_bigbed.bigbed" value="big_bed/myHub/Dbia3/tracks/BLAT_alignment_bigbed.bigbed" compare="sim_size" /> <expand macro="verify_hub_structure" test="big_bed"> <has_text text="searchIndex"/> <has_text text="searchTrix"/> </expand> <!-- check Trix index directory --> <extra_files type="file" name="myHub/Dbia3/trix/BLAT_alignment_bigbed.bigbed.ix" value="trix_index_files/blat_out.ix" /> <extra_files type="file" name="myHub/Dbia3/trix/BLAT_alignment_bigbed.bigbed.ixx" value="trix_index_files/blat_out.ixx" /> </output> </test> </tests> <help> This Galaxy tool permits to prepare your files to be ready for Assembly Hub visualization. </help> <citations> <citation type="doi">10.7490/f1000research.1112719.1</citation> </citations> </tool>