Mercurial > repos > yating-l > hubarchivecreator
changeset 85:a65e52152476 draft default tip
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
| author | yating-l |
|---|---|
| date | Mon, 06 Nov 2017 13:13:01 -0500 |
| parents | cb62314a6297 |
| children | |
| files | datatypes/binary/BigBed.py datatypes/binary/BigBed.pyc datatypes/interval/BigPsl.pyc hubArchiveCreator.xml macros.xml test-data/trix_index_files/bigbed_trackhub.html test-data/trix_index_files/blast_alignment_trackhub.html test-data/trix_index_files/blat_alignment_trackhub.html tests.xml util/index/TrixIndex.py util/index/TrixIndex.pyc |
| diffstat | 11 files changed, 127 insertions(+), 218 deletions(-) [+] |
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--- a/datatypes/binary/BigBed.py Fri Nov 03 17:08:19 2017 -0400 +++ b/datatypes/binary/BigBed.py Mon Nov 06 13:13:01 2017 -0500 @@ -37,7 +37,7 @@ self.database_settings = DatabaseIndex(database=self.trackSettings["database"], seqType=self.seqType).setExtLink() self.extraSettings.update(self.database_settings) if "index_ix" in self.trackSettings and "index_ixx" in self.trackSettings: - self.trix_id = self.extraSettings.get("trix_id") + self.trix_id = self.trackSettings.get("trix_id") if not self.trix_id: self.logger.info("Didn't specify the ID for Trix index for BigBed file: %s. \n Will use \"name\" as default", self.trackName) self.trix_id = "name"
--- a/hubArchiveCreator.xml Fri Nov 03 17:08:19 2017 -0400 +++ b/hubArchiveCreator.xml Mon Nov 06 13:13:01 2017 -0500 @@ -459,7 +459,8 @@ </outputs> <tests> - <!-- Test with only the fasta file --> + + <!-- Test with only the fasta file --> <test> <param name="genome_name" value="Dbia3"/> <param name="fasta_file" value="common/dbia3.fa"/> @@ -1374,9 +1375,9 @@ </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" /> + value="trix_index_files/blat_out.ix" /> <extra_files type="file" name="myHub/Dbia3/trix/BLAT_alignment_bigpsl.bb.ixx" - value="trix_index/blat_out.ixx" /> + value="trix_index_files/blat_out.ixx" /> </output> </test> @@ -1424,9 +1425,9 @@ </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" /> + value="trix_index_files/blast_out.ix" /> <extra_files type="file" name="myHub/Dbia3/trix/BLAST_alignment_bigpsl.bb.ixx" - value="trix_index/blast_out.ixx" /> + value="trix_index_files/blast_out.ixx" /> </output> </test> @@ -1444,7 +1445,7 @@ <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_index" value="trix_index_files/blat_out.ix,trix_index_files/blat_out.ixx" /> <param name="trix_id" value="name" /> </conditional> </conditional> @@ -1464,9 +1465,9 @@ <!-- check Trix index directory --> <extra_files type="file" name="myHub/Dbia3/trix/BLAT_alignment_bigbed.bigbed.ix" - value="trix_index/blat_out.ix" /> + value="trix_index_files/blat_out.ix" /> <extra_files type="file" name="myHub/Dbia3/trix/BLAT_alignment_bigbed.bigbed.ixx" - value="trix_index/blat_out.ixx" /> + value="trix_index_files/blat_out.ixx" /> </output> </test>
--- a/macros.xml Fri Nov 03 17:08:19 2017 -0400 +++ b/macros.xml Mon Nov 06 13:13:01 2017 -0500 @@ -63,14 +63,17 @@ type="data" format="txt" multiple="true" + min="2" + max="2" label="Specify Trix index" help="Dataset collection containing ix and ixx files generated by UCSC Trix Index Generator" /> - <yield /> + <yield /> </when> <when value="no"> </when> </conditional> </xml> + </macros> \ No newline at end of file
--- a/test-data/trix_index_files/bigbed_trackhub.html Fri Nov 03 17:08:19 2017 -0400 +++ b/test-data/trix_index_files/bigbed_trackhub.html Mon Nov 06 13:13:01 2017 -0500 @@ -26,27 +26,14 @@ <ul> <li> - <a href="myHub/Dbia3/groups.txt">groups.txt</a> - </li> - <li> <a href="myHub/Dbia3/Dbia3.2bit">Dbia3.2bit</a> </li> <li> - <a href="myHub/Dbia3/description.html">description.html</a> + <a href="myHub/Dbia3/trackDb.txt">trackDb.txt</a> </li> <li> - trix + <a href="myHub/Dbia3/groups.txt">groups.txt</a> </li> - <ul> - - <li> - <a href="myHub/unknown/trix/pslToBigPsl_on_data_43.bb.bigbed.ix">pslToBigPsl_on_data_43.bb.bigbed.ix</a> - </li> - <li> - <a href="myHub/unknown/trix/pslToBigPsl_on_data_43.bb.bigbed.ixx">pslToBigPsl_on_data_43.bb.bigbed.ixx</a> - </li> - - </ul> <li> tracks </li> @@ -58,8 +45,21 @@ </ul> <li> - <a href="myHub/Dbia3/trackDb.txt">trackDb.txt</a> + <a href="myHub/Dbia3/description.html">description.html</a> + </li> + <li> + trix </li> + <ul> + + <li> + <a href="myHub/Dbia3/trix/BLAT_alignment_bigbed.bigbed.ixx">BLAT_alignment_bigbed.bigbed.ixx</a> + </li> + <li> + <a href="myHub/Dbia3/trix/BLAT_alignment_bigbed.bigbed.ix">BLAT_alignment_bigbed.bigbed.ix</a> + </li> + + </ul> </ul>
--- a/test-data/trix_index_files/blast_alignment_trackhub.html Fri Nov 03 17:08:19 2017 -0400 +++ b/test-data/trix_index_files/blast_alignment_trackhub.html Mon Nov 06 13:13:01 2017 -0500 @@ -12,15 +12,27 @@ <ul> <li> - unknown + <a href="myHub/Dbia3.html">Dbia3.html</a> + </li> + <li> + <a href="myHub/genomes.txt">genomes.txt</a> + </li> + <li> + <a href="myHub/hub.txt">hub.txt</a> + </li> + <li> + Dbia3 </li> <ul> <li> - <a href="myHub/unknown/trackDb.txt">trackDb.txt</a> + <a href="myHub/Dbia3/Dbia3.2bit">Dbia3.2bit</a> </li> <li> - <a href="myHub/unknown/groups.txt">groups.txt</a> + <a href="myHub/Dbia3/trackDb.txt">trackDb.txt</a> + </li> + <li> + <a href="myHub/Dbia3/groups.txt">groups.txt</a> </li> <li> tracks @@ -33,34 +45,21 @@ </ul> <li> + <a href="myHub/Dbia3/description.html">description.html</a> + </li> + <li> trix </li> <ul> <li> - <a href="myHub/unknown/trix/BLAST_alignment_bigpsl.bb.ix">BLAST_alignment_bigpsl.bb.ix</a> + <a href="myHub/Dbia3/trix/BLAST_alignment_bigpsl.bb.ixx">BLAST_alignment_bigpsl.bb.ixx</a> </li> <li> - <a href="myHub/unknown/trix/BLAST_alignment_bigpsl.bb.ixx">BLAST_alignment_bigpsl.bb.ixx</a> + <a href="myHub/Dbia3/trix/BLAST_alignment_bigpsl.bb.ix">BLAST_alignment_bigpsl.bb.ix</a> </li> </ul> - <li> - tracks - </li> - <ul> - - <li> - <a href="myHub/Dbia3/tracks/BLAST_alignment_bigpsl.bb">BLAST_alignment_bigpsl.bb</a> - </li> - - </ul> - <li> - <a href="myHub/Dbia3/Dbia3.2bit">Dbia3.2bit</a> - </li> - <li> - <a href="myHub/Dbia3/description.html">description.html</a> - </li> </ul>
--- a/test-data/trix_index_files/blat_alignment_trackhub.html Fri Nov 03 17:08:19 2017 -0400 +++ b/test-data/trix_index_files/blat_alignment_trackhub.html Mon Nov 06 13:13:01 2017 -0500 @@ -12,15 +12,27 @@ <ul> <li> - unknown + <a href="myHub/Dbia3.html">Dbia3.html</a> + </li> + <li> + <a href="myHub/genomes.txt">genomes.txt</a> + </li> + <li> + <a href="myHub/hub.txt">hub.txt</a> + </li> + <li> + Dbia3 </li> <ul> <li> - <a href="myHub/unknown/trackDb.txt">trackDb.txt</a> + <a href="myHub/Dbia3/Dbia3.2bit">Dbia3.2bit</a> </li> <li> - <a href="myHub/unknown/groups.txt">groups.txt</a> + <a href="myHub/Dbia3/trackDb.txt">trackDb.txt</a> + </li> + <li> + <a href="myHub/Dbia3/groups.txt">groups.txt</a> </li> <li> tracks @@ -33,34 +45,21 @@ </ul> <li> + <a href="myHub/Dbia3/description.html">description.html</a> + </li> + <li> trix </li> <ul> <li> - <a href="myHub/unknown/trix/BLAT_alignment_bigpsl.bb.bigbed.ix">BLAT_alignment_bigpsl.bb.ix</a> + <a href="myHub/Dbia3/trix/BLAT_alignment_bigpsl.bb.ix">BLAT_alignment_bigpsl.bb.ix</a> </li> <li> - <a href="myHub/unknown/trix/BLAT_alignment_bigpsl.bb.bigbed.ixx">BLAT_alignment_bigpsl.bb.ixx</a> + <a href="myHub/Dbia3/trix/BLAT_alignment_bigpsl.bb.ixx">BLAT_alignment_bigpsl.bb.ixx</a> </li> </ul> - <li> - tracks - </li> - <ul> - - <li> - <a href="myHub/Dbia3/tracks/BLAT_alignment_bigpsl.bb">BLAT_alignment_bigpsl.bb</a> - </li> - - </ul> - <li> - <a href="myHub/Dbia3/Dbia3.2bit">Dbia3.2bit</a> - </li> - <li> - <a href="myHub/Dbia3/description.html">description.html</a> - </li> </ul>
--- a/tests.xml Fri Nov 03 17:08:19 2017 -0400 +++ b/tests.xml Mon Nov 06 13:13:01 2017 -0500 @@ -1,6 +1,59 @@ -<macro> - <xml name="test_cases"> - <!-- Test with only the fasta file --> + #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"/> @@ -870,149 +923,3 @@ <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition --> </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 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> - - <!-- 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> - - <!-- Test for big files? --> - - <!-- Find tests that should fail --> - </xml> -</macro>
--- a/util/index/TrixIndex.py Fri Nov 03 17:08:19 2017 -0400 +++ b/util/index/TrixIndex.py Mon Nov 06 13:13:01 2017 -0500 @@ -14,7 +14,7 @@ self.trackName = trackName self.mySpecieFolderPath = mySpecieFolderPath self.index_settings = collections.OrderedDict() - self.trixId = trixId + self.trixId = trixId.rstrip() def setExtLink(self):