Mercurial > repos > yating-l > hubarchivecreator
diff hubArchiveCreator.xml @ 66:4ca7cbf2d9b8 draft
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 159730602ff500b59aefc7080fb49b726c88d655-dirty
| author | yating-l |
|---|---|
| date | Tue, 26 Sep 2017 16:44:58 -0400 |
| parents | e50fc56bd10d |
| children | 39a32cb31623 |
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--- a/hubArchiveCreator.xml Wed Aug 09 16:40:21 2017 -0400 +++ b/hubArchiveCreator.xml Tue Sep 26 16:44:58 2017 -0400 @@ -3,6 +3,9 @@ This Galaxy tool permits to prepare your files to be ready for Assembly Hub visualization. </description> + <macros> + <import>macros.xml</import> + </macros> <requirements> <requirement type="package" version="340">ucsc_hac</requirement> @@ -23,160 +26,154 @@ <!-- Idea: python \ -augustus [parameters] \ -trfBig [parameters] --> <command detect_errors="exit_code"><![CDATA[ mkdir -p $output.extra_files_path; + + ## Dump the tool parameters into a JSON file + python $json_file parameters.json; - python $__tool_directory__/hubArchiveCreator.py + python $__tool_directory__/hubArchiveCreator.py --data_json parameters.json -o $output; + - ## Ask the user to enter the genome name - --genome_name '$genome_name' + ]]></command> + <configfiles> + <configfile name="json_file"> +import json +import sys - #import json +file_path = sys.argv[1] +#set global $data_parameter_dict = {} - #set global data_parameter_dict = {} +## Ask the user to enter the genome name +#silent $data_parameter_dict.update({"genome_name": str($genome_name)}) + +## Function to retrieve the data of the inputs +#def prepare_json($datatype, $input_to_prepare, $order_index, $extra_data_dict={}) + #set false_path = str($input_to_prepare) + #set $data_dict = {"false_path": $false_path} - ## Function to retrieve the data of the inputs - #def prepare_json($input_to_prepare, $order_index, $extra_data_dict={}) - #set false_path = str($input_to_prepare) - #set name = $input_to_prepare.name + #set name = str($input_to_prepare.name) + #silent $data_dict.update({"name": $name}) + #silent $data_dict.update($extra_data_dict) + ## Add the ordering by taking the tool form indexes + #silent $data_dict.update({"order_index": $order_index}) - #set data_dict = {"name": $name} - #silent data_dict.update($extra_data_dict) + #if $datatype in $data_parameter_dict + #silent $data_parameter_dict[$datatype].append($data_dict) + #else + #set array_inputs = [] + #silent $array_inputs.append($data_dict) + #silent $data_parameter_dict.update({$datatype: $array_inputs}) + #end if +#end def - ## Add the ordering by taking the tool form indexes - #silent $data_dict.update({"order_index": $order_index}) +## Get the number of digits from tracks, to have a unique integer from group index and track index + +#set temp_max_digit = 0 - #silent $data_parameter_dict.update({$false_path: $data_dict}) - - #end def +#for $g in $group + #if len($g.format) > $temp_max_digit + #silent temp_max_digit = len($g.format) + #end if +#end for - ## Get the number of digits from tracks, to have a unique integer from group index and track index +#set nb_digits_max_track = len(str($temp_max_digit)) - #set temp_max_digit = 0 +## END Get the number of digits - #for $g in $group - #if len($g.format) > $temp_max_digit - #silent temp_max_digit = len($g.format) - #end if - #end for - - #set nb_digits_max_track = len(str($temp_max_digit)) - - ## END Get the number of digits +#for $i_g, $g in enumerate( $group ) + #for $i, $f in enumerate( $g.format ) + ## Create the order index using index_group+1 concatenated with index_track + #set index_group_final = str($i_g + 1) + #set index_track_final = str($index_group_final) + str($i).zfill($nb_digits_max_track) - #for $i_g, $g in enumerate( $group ) - #for $i, $f in enumerate( $g.format ) - ## Create the order index using index_group+1 concatenated with index_track - #set index_group_final = str($i_g + 1) - #set index_track_final = str($index_group_final) + str($i).zfill($nb_digits_max_track) + ## For each format, we have a few mandatory fields we store in a dict + #set track_color = str($f.formatChoice.track_color) + #set group_name = str($g.group_name) + #set longLabel = str($f.formatChoice.longLabel) + #set extra_data_dict = {"track_color": $track_color, + "group_name": $group_name, + "long_label": $longLabel} - ## For each format, we have a few mandatory fields we store in a dict - #set track_color = str($f.formatChoice.track_color) - #set group_name = str($g.group_name) - #set longLabel = str($f.formatChoice.longLabel) - #set extra_data_dict = {"database": "", - "track_color": $track_color, - "group_name": $group_name, - "long_label": $longLabel} + #if $f.formatChoice.format_select == "bam" + #set bam_index = $f.formatChoice.BAM.metadata.bam_index - #if $f.formatChoice.format_select == "bam" - --bam $f.formatChoice.BAM - #set bam_index = $f.formatChoice.BAM.metadata.bam_index - - ## Add Bam format specific fields - #silent extra_data_dict.update({"index": $bam_index}) + ## Add Bam format specific fields + #silent $extra_data_dict.update({"index": $bam_index}) - #silent $prepare_json($f.formatChoice.BAM, $index_track_final, extra_data_dict) - #end if - #if $f.formatChoice.format_select == "bed" - #if $f.formatChoice.bedChoice.bed_select == "bed_generic" - --bed $f.formatChoice.bedChoice.BED - #silent $prepare_json($f.formatChoice.bedChoice.BED, $index_track_final, - extra_data_dict) - #end if - #if $f.formatChoice.bedChoice.bed_select == "bed_cytoBand" - --cytoBand $f.formatChoice.bedChoice.BED_cytoBand - #silent $prepare_json($f.formatChoice.bedChoice.BED_cytoBand, $index_track_final, - extra_data_dict) - #end if - #if $f.formatChoice.bedChoice.bed_select == "bed_simple_repeats_option" - --bedSimpleRepeats $f.formatChoice.bedChoice.BED_simple_repeats - #silent $prepare_json($f.formatChoice.bedChoice.BED_simple_repeats, $index_track_final, - extra_data_dict) - #end if - #if $f.formatChoice.bedChoice.bed_select == "bed_splice_junctions_option" - --bedSpliceJunctions $f.formatChoice.bedChoice.BED_splice_junctions - #silent $prepare_json($f.formatChoice.bedChoice.BED_splice_junctions, $index_track_final, - extra_data_dict) - #end if - #if $f.formatChoice.bedChoice.bed_select == "bed_blast_alignment_option" - --bedBlastAlignments $f.formatChoice.bedChoice.BED_blast_alignment - #set database = str($f.formatChoice.bedChoice.database) - #silent extra_data_dict.update({"database": $database}) - #silent $prepare_json($f.formatChoice.bedChoice.BED_blast_alignment, $index_track_final, - extra_data_dict) - #end if - #if $f.formatChoice.bedChoice.bed_select == "bed_blat_alignment_option" - --bigpsl $f.formatChoice.bedChoice.BED_blat_alignment - #if $f.formatChoice.bedChoice.if_index.if_index_selector == "true" - #set search_index = $f.formatChoice.bedChoice.if_index.search_index - #silent extra_data_dict.update({"search_index": $search_index}) - #end if - #set database = str($f.formatChoice.bedChoice.database) - #silent extra_data_dict.update({"database": $database}) - #silent $prepare_json($f.formatChoice.bedChoice.BED_blat_alignment, $index_track_final, - extra_data_dict) - #end if - #end if - #if $f.formatChoice.format_select == "psl" - --psl $f.formatChoice.PSL - #silent $prepare_json($f.formatChoice.PSL, $index_track_final, - extra_data_dict) - #end if - #if $f.formatChoice.format_select == "bigwig" - --bigwig $f.formatChoice.BIGWIG - #silent $prepare_json($f.formatChoice.BIGWIG, $index_track_final, - extra_data_dict) - #end if - #if $f.formatChoice.format_select == "bigbed" - --bigbed $f.formatChoice.BIGBED - #silent $prepare_json($f.formatChoice.BIGBED, $index_track_final, - extra_data_dict) - #end if - #if $f.formatChoice.format_select == "gff3" - --gff3 $f.formatChoice.GFF3 - #silent $prepare_json($f.formatChoice.GFF3, $index_track_final, - extra_data_dict) - #end if - #if $f.formatChoice.format_select == "gtf" - ## Add also GTF from Agustus? See https://github.com/ENCODE-DCC/kentUtils/issues/8 - --gtf $f.formatChoice.GTF - #silent $prepare_json($f.formatChoice.GTF, $index_track_final, - extra_data_dict) - #end if - #end for - #end for + #silent $prepare_json("Bam", $f.formatChoice.BAM, $index_track_final, $extra_data_dict) + #end if + #if $f.formatChoice.format_select == "bed" + #if $f.formatChoice.bedChoice.bed_select == "bed_generic" + #silent $prepare_json("Bed", $f.formatChoice.bedChoice.BED, $index_track_final, + $extra_data_dict) + #end if + #if $f.formatChoice.bedChoice.bed_select == "bed_cytoBand" + #silent $prepare_json("CytoBand", $f.formatChoice.bedChoice.BED_cytoBand, $index_track_final, + $extra_data_dict) + #end if + #if $f.formatChoice.bedChoice.bed_select == "bed_simple_repeats_option" + #silent $prepare_json("BedSimpleRepeats", $f.formatChoice.bedChoice.BED_simple_repeats, $index_track_final, + $extra_data_dict) + #end if + #if $f.formatChoice.bedChoice.bed_select == "bed_splice_junctions_option" + #silent $prepare_json("BedSpliceJunctions", $f.formatChoice.bedChoice.BED_splice_junctions, $index_track_final, + $extra_data_dict) + #end if + #if $f.formatChoice.bedChoice.bed_select == "bed_blast_alignment_option" + #set database = str($f.formatChoice.bedChoice.database) + #silent $extra_data_dict.update({"database": $database}) + #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}) + #silent $prepare_json("BedBlatAlignments", $f.formatChoice.bedChoice.BED_blat_alignment, $index_track_final, + $extra_data_dict) + #end if + #end if + #if $f.formatChoice.format_select == "psl" + #silent $prepare_json("Psl", $f.formatChoice.PSL, $index_track_final, + $extra_data_dict) + #end if + #if $f.formatChoice.format_select == "bigwig" + #silent $prepare_json("BigWig", $f.formatChoice.BIGWIG, $index_track_final, + $extra_data_dict) + #end if + #if $f.formatChoice.format_select == "bigbed" + #silent $prepare_json("BigBed", $f.formatChoice.BIGBED, $index_track_final, + $extra_data_dict) + #end if + #if $f.formatChoice.format_select == "gff3" + #silent $prepare_json("Gff3", $f.formatChoice.GFF3, $index_track_final, + $extra_data_dict) + #end if + #if $f.formatChoice.format_select == "gtf" + ## Add also GTF from Agustus? See https://github.com/ENCODE-DCC/kentUtils/issues/8 + #silent $prepare_json("Gtf", $f.formatChoice.GTF, $index_track_final, + $extra_data_dict) + #end if + #end for +#end for - ## We combine the fasta file dataset name with his false path in a JSON object - #set fasta_json = json.dumps({"false_path": str($fasta_file), "name": $fasta_file.name}) - -f '$fasta_json' +## We combine the fasta file dataset name with his false path in a JSON object +#set fasta_json = {"false_path": str($fasta_file), "name": str($fasta_file.name)} +$data_parameter_dict.update({"fasta": $fasta_json}) - ## Dump the final json - #set all_data_json = json.dumps($data_parameter_dict) +## Retrieve the user email +#silent $data_parameter_dict.update({"user_email": str($__user_email__)}) - --data_json '$all_data_json' +#silent $data_parameter_dict.update({"tool_directory": str($__tool_directory__)}) - ## Retrieve the user email - --user_email $__user_email__ +#silent $data_parameter_dict.update({"extra_files_path": str($output.extra_files_path)}) - -d $__tool_directory__ +#silent $data_parameter_dict.update({"debug_mode": str($advanced_options.debug_mode)}) - -e $output.extra_files_path - - $advanced_options.debug_mode +with open(file_path, 'w') as f: + json.dump($data_parameter_dict, f) - -o $output; - - ]]></command> + </configfile> + </configfiles> <inputs> <param @@ -290,17 +287,7 @@ <param name="database" type="select" label="mRNA database"> <option value="NCBI" selected="true">NCBI</option> <option value="Others">Others</option> - </param> - <conditional name="if_index"> - <param name="if_index_selector" type="select" label="Provide TRIX file for searchTrix"> - <option value="true" selected="True">Provide TRIX file</option> - <option value="false">Don't provide TRIX file</option> - </param> - <when value="true"> - <param format="txt" name="search_index" type="data" label="trix index file" /> - </when> - <when value="false"></when> - </conditional> + </param> </when> </conditional> <param name="longLabel" type="text" size="76" label="Track label" help="It is limited to 76 printable characters, the first 17 printable characters will be used as a short label of the track" /> @@ -402,9 +389,9 @@ </param> <!-- TODO: Avoid redundancy here --> <when value="on"> - <param name="debug_mode" type="boolean" - label="Activate debug mode" checked="false" - truevalue="--debug_mode" falsevalue=""> + <param name="debug_mode" type="select" label="Activate debug mode"> + <option value="false" selected="true">No</option> + <option value="true">Yes</option> <help> Use this option if you are a G-OnRamp developer </help> @@ -412,11 +399,11 @@ </when> <when value="off"> <param name="debug_mode" type="hidden" - value=""> + value="false"> </param> </when> - </conditional> -</inputs> + </conditional> + </inputs> <outputs> <data format="trackhub" name="output"/> @@ -428,18 +415,8 @@ <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"/> + <!-- Use macro to check the whole common structure without repeated code --> + <expand macro="verify_hub_structure_no_track" test="only_genome" /> </output> </test> @@ -453,6 +430,7 @@ <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> @@ -469,22 +447,8 @@ 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 --> + <!-- Use macro to check the whole common structure without repeated code --> + <expand macro="verify_hub_structure" test="bam" /> </output> </test> @@ -500,18 +464,19 @@ <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"> - <!-- 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" /> + <expand macro="verify_hub_structure" test="bed_generic" /> </output> </test> @@ -527,22 +492,22 @@ <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"> - <!-- 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" /> + <expand macro="verify_hub_structure" test="bed_simple_repeats" /> </output> </test> - <!-- Test with Psl --> <test> <param name="genome_name" value="Dbia3"/> @@ -553,19 +518,18 @@ <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"> - <!-- 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 --> + <expand macro="verify_hub_structure" test="psl" /> </output> </test> @@ -578,20 +542,27 @@ <repeat name="format"> <conditional name="formatChoice"> <param name="format_select" value="bigwig"/> - <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Summary"/> + <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"> - <!-- 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" + name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig" + value="bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.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 --> + <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> @@ -605,19 +576,18 @@ <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"> - <!-- 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 --> + <expand macro="verify_hub_structure" test="gff3" /> </output> </test> @@ -631,19 +601,182 @@ <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"> - <!-- 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 --> + <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> @@ -669,7 +802,6 @@ </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" @@ -680,12 +812,11 @@ 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 --> + <expand macro="verify_hub_structure" test="gtf_gff" /> </output> </test> - <!-- Test with one group and all the supported datatypes on 10/04/2016 --> + <!-- Test with one group and all the supported datatypes --> <test> <param name="genome_name" value="Dbia3"/> <param name="fasta_file" value="common/dbia3.fa"/> @@ -729,7 +860,7 @@ <repeat name="format"> <conditional name="formatChoice"> <param name="format_select" value="bigwig"/> - <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Summary"/> + <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Coverage"/> <param name="track_color" value="#000000"/> </conditional> </repeat> @@ -747,6 +878,48 @@ <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 --> @@ -776,8 +949,8 @@ 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" + 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" @@ -790,12 +963,31 @@ 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 --> + <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 with two groups and no tracks --> <test> <param name="genome_name" value="Dbia3"/> <param name="fasta_file" value="common/dbia3.fa"/> @@ -806,18 +998,7 @@ <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"/> + <expand macro="verify_hub_structure_no_track" test="two_groups_no_track" /> </output> </test> @@ -830,7 +1011,7 @@ <repeat name="format"> <conditional name="formatChoice"> <param name="format_select" value="bigwig"/> - <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Summary"/> + <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Coverage"/> <param name="track_color" value="#000000"/> </conditional> </repeat> @@ -839,28 +1020,13 @@ <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" + name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig" + value="bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig" compare="sim_size" /> - - <!-- Check the groups.txt exists and is properly populated --> + <expand macro="verify_hub_structure" test="two_groups_one_track_first" /> </output> </test> @@ -873,7 +1039,7 @@ <repeat name="format"> <conditional name="formatChoice"> <param name="format_select" value="bigwig"/> - <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Summary"/> + <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Coverage"/> <param name="track_color" value="#000000"/> </conditional> </repeat> @@ -889,26 +1055,11 @@ </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" + name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig" + value="bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig" compare="sim_size" /> @@ -918,6 +1069,7 @@ 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> @@ -931,7 +1083,7 @@ <repeat name="format"> <conditional name="formatChoice"> <param name="format_select" value="bigwig"/> - <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Summary"/> + <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Coverage"/> <param name="track_color" value="#000000"/> </conditional> </repeat> @@ -961,26 +1113,11 @@ </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" + 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" @@ -1005,7 +1142,7 @@ 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 --> + <expand macro="verify_hub_structure" test="two_groups_multiple_tracks" /> </output> </test> @@ -1024,8 +1161,9 @@ </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" value="default_color/myHub/Dbia3/trackDb.txt"> + <extra_files type="file" name="myHub/Dbia3/trackDb.txt"> <assert_contents> <has_text text="color 0,0,0"/> </assert_contents> @@ -1050,8 +1188,9 @@ </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" value="changed_color/myHub/Dbia3/trackDb.txt"> + <extra_files type="file" name="myHub/Dbia3/trackDb.txt"> <assert_contents> <has_text text="color 128,100,162"/> </assert_contents> @@ -1081,11 +1220,70 @@ value="stringtie_chromosome_end_coordinates/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb" compare="sim_size" /> + <expand macro="verify_hub_structure" test="stringtie_chromosome_end_coordinates" /> + + <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition --> + </output> + </test> + + <!-- Test default label in a track --> + <test> + <param name="genome_name" value="Dbia3"/> + <param name="fasta_file" value="common/dbia3.fa"/> + <repeat name="group"> + <param name="group_name" value="Default group"/> + <repeat name="format"> + <conditional name="formatChoice"> + <param name="format_select" value="bam"/> + <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam"/> + <param name="track_color" value="#000000"/> + </conditional> + </repeat> + </repeat> + <output name="output" file="default_color/default_color_trackhub.html"> + <expand macro="verify_hub_structure" test="default_color" /> + <!-- Verify trackDb.txt contains default label --> + <extra_files type="file" name="myHub/Dbia3/trackDb.txt"> + <assert_contents> + <has_text text="longLabel HISAT2 Accepted Hits.bam"/> + </assert_contents> + </extra_files> <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition --> </output> </test> + <!-- Test customized label in a track --> + <test> + <param name="genome_name" value="Dbia3"/> + <param name="fasta_file" value="common/dbia3.fa"/> + <repeat name="group"> + <param name="group_name" value="Default group"/> + <repeat name="format"> + <conditional name="formatChoice"> + <param name="format_select" value="bam"/> + <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam"/> + <param name="longLabel" value="HISAT sequence alignment" /> + <param name="track_color" value="#000000"/> + </conditional> + </repeat> + </repeat> + <output name="output" file="changed_label/changed_label_trackhub.html"> + <expand macro="verify_hub_structure" test="changed_label" /> + <!-- Verify trackDb.txt contains the customized label --> + <extra_files type="file" name="myHub/Dbia3/trackDb.txt"> + <assert_contents> + <has_text text="longLabel HISAT sequence alignment"/> + </assert_contents> + </extra_files> + + <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition --> + </output> + </test> + + + + <!-- Test for big files? --> <!-- Find tests that should fail -->