Mercurial > repos > rmarenco > hubarchivecreator
diff tests.xml @ 29:7e8a8b732db3 draft
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
| author | yating-l |
|---|---|
| date | Wed, 16 May 2018 18:04:20 -0400 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tests.xml Wed May 16 18:04:20 2018 -0400 @@ -0,0 +1,925 @@ + #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>