Mercurial > repos > rmarenco > hubarchivecreator
view tests.xml @ 30:e7c4be523cb7 draft
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 2f1b3cc8c9cb463e460f7f79efe99ed472700ecf
| author | yating-l |
|---|---|
| date | Tue, 19 Jun 2018 13:02:32 -0400 |
| parents | 7e8a8b732db3 |
| children |
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#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 #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 <!-- 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>