Mercurial > repos > yating-l > hubarchivecreator
diff hubArchiveCreator.xml @ 84:cb62314a6297 draft
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
| author | yating-l |
|---|---|
| date | Fri, 03 Nov 2017 17:08:19 -0400 |
| parents | 0bc486356e2a |
| children | a65e52152476 |
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--- a/hubArchiveCreator.xml Mon Oct 30 12:01:23 2017 -0400 +++ b/hubArchiveCreator.xml Fri Nov 03 17:08:19 2017 -0400 @@ -123,9 +123,16 @@ #set database = str($f.formatChoice.bedChoice.database) #silent $extra_data_dict.update({"database": $database}) #if $f.formatChoice.bedChoice.add_trix_index.add_trix_index_selector == "yes" - #set ix_index = str($f.formatChoice.bedChoice.add_trix_index.add_trix_file.trix_index.index_ix) - #set ixx_index = str($f.formatChoice.bedChoice.add_trix_index.add_trix_file.trix_index.index_ixx) - #silent $extra_data_dict.update({"indexIx": $ix_index, "indexIxx": $ixx_index}) + #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, $extra_data_dict) @@ -134,9 +141,16 @@ #set database = str($f.formatChoice.bedChoice.database) #silent $extra_data_dict.update({"database": $database}) #if $f.formatChoice.bedChoice.add_trix_index.add_trix_index_selector == "yes" - #set ix_index = str($f.formatChoice.bedChoice.add_trix_index.add_trix_file.trix_index.index_ix) - #set ixx_index = str($f.formatChoice.bedChoice.add_trix_index.add_trix_file.trix_index.index_ixx) - #silent $extra_data_dict.update({"indexIx": $ix_index, "indexIxx": $ixx_index}) + #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) @@ -152,10 +166,18 @@ #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.add_trix_file.trix_index.index_ix) - #set ixx_index = str($f.formatChoice.add_trix_index.add_trix_file.trix_index.index_ixx) - #set trix_id = str($f.formatChoice.add_trix_index.add_trix_file.trix_id) - #silent $extra_data_dict.update({"indexIx": $ix_index, "indexIxx": $ixx_index, "trix_id": $trix_id}) + ##set ix_index = str($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) @@ -362,7 +384,7 @@ value="name" type="text" size="30" - label="Specify Trix identifier" + label="Specify Trix identifier (The default is name)" /> </expand> <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" /> @@ -1308,13 +1330,146 @@ </output> </test> - - + <!-- Test TrixIndex for Blat alignment 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="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 name="add_trix_index"> + <param name="add_trix_index_selector" value="yes" /> + <param name="trix_index" value="trix_index_files/blat_out.ix,trix_index_files/blat_out.ixx" /> + </conditional> + </conditional> + </conditional> + </repeat> + </repeat> + <param name="debug_mode" value="true" /> + <output name="output" file="trix_index_files/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="searchTrix"/> + <has_text text="url"/> + <has_text text="urlLabel"/> + <has_text text="iframeUrl"/> + <has_text text="iframeOptions"/> + </assert_contents> + </extra_files> + <!-- check Trix index directory --> + <extra_files type="file" name="myHub/Dbia3/trix/BLAT_alignment_bigpsl.bb.ix" + value="trix_index/blat_out.ix" /> + <extra_files type="file" name="myHub/Dbia3/trix/BLAT_alignment_bigpsl.bb.ixx" + value="trix_index/blat_out.ixx" /> + </output> + </test> - <!-- Test for big files? --> + <!-- Test TrixIndex for 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 name="add_trix_index"> + <param name="add_trix_index_selector" value="yes" /> + <param name="trix_index" value="trix_index_files/blast_out.ix,trix_index_files/blast_out.ixx" /> + </conditional> + </conditional> + </conditional> + </repeat> + </repeat> + <param name="debug_mode" value="true" /> + <output name="output" file="trix_index_files/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="searchTrix"/> + <has_text text="url"/> + <has_text text="urlLabel"/> + <has_text text="iframeUrl"/> + <has_text text="iframeOptions"/> + </assert_contents> + </extra_files> + <!-- check Trix index directory --> + <extra_files type="file" name="myHub/Dbia3/trix/BLAST_alignment_bigpsl.bb.ix" + value="trix_index/blast_out.ix" /> + <extra_files type="file" name="myHub/Dbia3/trix/BLAST_alignment_bigpsl.bb.ixx" + value="trix_index/blast_out.ixx" /> + </output> + </test> - <!-- Find tests that should fail --> + <!-- Test TrixIndex for 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 name="add_trix_index"> + <param name="add_trix_index_selector" value="yes" /> + <param name="trix_index" value="trix_index_files/blast_out.ix,trix_index_files/blast_out.ixx" /> + <param name="trix_id" value="name" /> + </conditional> + </conditional> + </repeat> + </repeat> + <param name="debug_mode" value="true" /> + <output name="output" file="trix_index_files/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"> + <has_text text="searchIndex"/> + <has_text text="searchTrix"/> + </expand> + <!-- check Trix index directory --> + <extra_files type="file" name="myHub/Dbia3/trix/BLAT_alignment_bigbed.bigbed.ix" + value="trix_index/blat_out.ix" /> + <extra_files type="file" name="myHub/Dbia3/trix/BLAT_alignment_bigbed.bigbed.ixx" + value="trix_index/blat_out.ixx" /> + </output> + </test> + </tests> <help>