Mercurial > repos > yating-l > hubarchivecreator
diff hubArchiveCreator.xml @ 2:4ced8f116509 draft
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty
| author | yating-l |
|---|---|
| date | Tue, 22 Nov 2016 17:13:18 -0500 |
| parents | 3e0c61b52a06 |
| children | 44577d6784b7 |
line wrap: on
line diff
--- a/hubArchiveCreator.xml Tue Nov 22 17:07:47 2016 -0500 +++ b/hubArchiveCreator.xml Tue Nov 22 17:13:18 2016 -0500 @@ -442,7 +442,33 @@ /> </output> </test> + <!-- Test with Psl --> + <test> + <param name="genome_name" value="Dbia3"/> + <param name="fasta_file" value="common/dbia3.fa"/> + <repeat name="group"> + <param name="group_name" value="Default group"/> + <repeat name="format"> + <conditional name="formatChoice"> + <param name="format_select" value="psl"/> + <param name="PSL" value="psl/inputs/blastXmlToPsl"/> + <param name="track_color" value="#000000"/> + </conditional> + </repeat> + </repeat> + <output name="output" file="psl/psl_trackhub.html"> + <!-- Verify tracks folder contains bam and bai --> + <extra_files type="file" + name="myHub/Dbia3/tracks/blastXmlToPsl.bb" + value="psl/myHub/Dbia3/tracks/blastXmlToPsl.bb" + compare="sim_size" + /> + <!-- Verify trackDb.txt contains the basic fields for a bam --> + <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition --> + </output> + </test> + <!-- Test with BigWig --> <test> <param name="genome_name" value="Dbia3"/> @@ -560,6 +586,114 @@ </test> <!-- Test with one group and all the supported datatypes on 10/04/2016 --> + <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_Summary"/> + <param name="track_color" value="#000000"/> + </conditional> + </repeat> + <repeat name="format"> + <conditional name="formatChoice"> + <param name="format_select" value="gff3"/> + <param name="GFF3" value="gff3/inputs/Augustus_Gene_Predictions"/> + <param name="track_color" value="#000000"/> + </conditional> + </repeat> + <repeat name="format"> + <conditional name="formatChoice"> + <param name="format_select" value="gtf"/> + <param name="GTF" value="gtf/inputs/StringTie_Assembled_Transcripts"/> + <param name="track_color" value="#000000"/> + </conditional> + </repeat> + </repeat> + <output name="output" file="all_datatypes/all_datatypes_trackhub.html"> + <!-- verify tracks folder contains all the files --> + <extra_files type="file" + name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam" + value="all_datatypes/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam" + compare="sim_size" + /> + <extra_files type="file" + name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai" + value="all_datatypes/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai" + compare="sim_size" + /> + <extra_files type="file" + name="myHub/Dbia3/tracks/TBLASTN_Alignment_to_proteins.bb" + value="all_datatypes/myHub/Dbia3/tracks/TBLASTN_Alignment_to_proteins.bb" + compare="sim_size" + /> + <extra_files type="file" + name="myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb" + value="all_datatypes/myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb" + compare="sim_size" + /> + <extra_files type="file" + name="myHub/Dbia3/tracks/blastXmlToPsl.bb" + value="all_datatypes/myHub/Dbia3/tracks/blastXmlToPsl.bb" + compare="sim_size" + /> + <extra_files type="file" + name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig" + value="all_datatypes/myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig" + compare="sim_size" + /> + <extra_files type="file" + name="myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb" + value="all_datatypes/myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb" + compare="sim_size" + /> + <extra_files type="file" + name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb" + value="all_datatypes/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb" + compare="sim_size" + /> + <!-- verify trackdb.txt contains the basic fields for a bam --> + <!-- todo: find a way to check also that the whole common structure is intact too, without too much repetition --> + </output> + </test> <!-- Test with two groups and no tracks --> <test> @@ -851,34 +985,8 @@ <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition --> </output> </test> - - <!-- Test for Bed to 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="bed" /> - <conditional name="bedChoice"> - <param name="bed_select" value="bed_generic"/> - <param name="BED" ftype="bed" value="bed_generic/inputs/testing"/> - <param name="track_color" value="#000000"/> - </conditional> - </conditional> - </repeat> - </repeat> - <output name="output" file="bed_generic/bed_generic2.html"> - <!-- Verify tracks folder contains bam and bai --> - <extra_files type="file" - name="myHub/Dbia3/tracks/testing.bb" - value="bed_generic/myHub/Dbia3/tracks/testing.bb" - compare="sim_size" - /> - </output> - </test> - + + <!-- Test for big files? --> <!-- Find tests that should fail -->