Mercurial > repos > yating-l > hubarchivecreator
diff tests.xml @ 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 |
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--- 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>