Mercurial > repos > rmarenco > hubarchivecreator
diff hubArchiveCreator.xml @ 20:40469b265ddb draft
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
| author | yating-l |
|---|---|
| date | Fri, 20 Jan 2017 17:12:03 -0500 |
| parents | d786bca6a75d |
| children | 884ee2a71680 |
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--- a/hubArchiveCreator.xml Thu Oct 13 22:49:01 2016 -0400 +++ b/hubArchiveCreator.xml Fri Jan 20 17:12:03 2017 -0500 @@ -5,24 +5,7 @@ </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="1.0">ucsc_tools_340</requirement> <requirement type="package" version="1.2">samtools</requirement> </requirements> @@ -38,6 +21,7 @@ <!-- 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 @@ -100,7 +84,7 @@ #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" + #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) @@ -110,6 +94,16 @@ #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 + #if $f.formatChoice.bedChoice.bed_select == "bigpsl_option" + --bigpsl $f.formatChoice.bedChoice.bigPsl + #silent $prepare_json($f.formatChoice.bedChoice.bigPsl, $index_track_final, + extra_data_dict) + #end if #end if #if $f.formatChoice.format_select == "psl" --psl $f.formatChoice.PSL @@ -149,11 +143,12 @@ -d $__tool_directory__ - -e $output.files_path + -e $output.extra_files_path $advanced_options.debug_mode -o $output; + ]]></command> <inputs> @@ -202,10 +197,12 @@ <when value="bed"> <conditional name="bedChoice"> <param name="bed_select" type="select" label="Bed Choice"> - <option value="bed" selected="true">BED Generic (bed3+)</option> + <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> + <option value="bigpsl_option">bigPsl (bed12+12 / bigPsl.as)</option> </param> - <when value="bed"> + <when value="bed_generic"> <param format="bed" name="BED" @@ -222,6 +219,22 @@ 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="bigpsl_option"> + <param + format="bed" + name="bigPsl" + type="data" + label="bigPsl (Bed12+12) File" + /> + </when> </conditional> <param name="track_color" type="color" label="Track color" value="#000000"> <sanitizer> @@ -322,52 +335,673 @@ </outputs> <tests> - <!-- Can also use assert_command to test command --> - <!-- Testing GFF3 input --> + <!-- 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="fasta_file" value="dbia3.fa"/> - <repeat name="format"> - <conditional name="formatChoice"> - <param name="format_select" value="gff3"/> - <param name="GFF3" value="augustusDbia3.gff3"/> - </conditional> + <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> - <repeat name="format"> - <param name="BED_simple_repeats" value="dbia3_trfBig_unsorted.bed"/> - <!-- TODO: Ask why the tests are not passing with this xml: - Error creating a job for these tool inputs - Error executing tool: 'NoneType' object has no attribute 'current_history' - <conditional name="formatChoice"> - <param name="format_select" value="bed"/> - <conditional name="bedChoice"> - <param name="bed_select" value="bed_simple_repeats_option"/> - <param name="BED_simple_repeats" value="dbia3_trfBig_unsorted.bed"/> + <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> - </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> - <output name="output"> - <assert_contents> - <has_text text="myHub"/> - </assert_contents> - <assert_contents> - <has_text text="dbia3_trfBig.bb"/> - </assert_contents> - <assert_contents> - <has_text text="SAODOAii qwwqod92921"/> - </assert_contents> + <!-- 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="fasta_file" value="dbia3.fa"/> - <param name="GFF3" value="augustusDbia3.gff3"/> - <output name="output" file="augustusOutput.html" lines_diff="2"> - <extra_files type="directory" value="myHub"/> - <extra_files type="file" name="myHub/dbia3/tracks/augustusDbia3.bb" value="augustusDbia3.bb"/> + <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> - <!-- Testing Generic BED input --> - <!-- Testing Bed Simple repeat input --> + + <!-- 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>