Mercurial > repos > iuc > gtftobed12
comparison gtfToBed12.xml @ 2:b026dae67fba draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtfToBed12 commit 2f9e5a51a632217e4966aa3b8e9d2b88a09a36e3"
| author | iuc |
|---|---|
| date | Thu, 20 Feb 2020 13:45:34 -0500 |
| parents | 57d45064f114 |
| children |
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| 1:57d45064f114 | 2:b026dae67fba |
|---|---|
| 62 </conditional> | 62 </conditional> |
| 63 </inputs> | 63 </inputs> |
| 64 <outputs> | 64 <outputs> |
| 65 <data name="bed_file" format="bed12" metadata_source="gtf_file" label="${tool.name} on ${on_string}: BED12"/> | 65 <data name="bed_file" format="bed12" metadata_source="gtf_file" label="${tool.name} on ${on_string}: BED12"/> |
| 66 <data name="transcript_info_file" format="tabular" metadata_source="gtf_file" label="${tool.name} on ${on_string}: Table"> | 66 <data name="transcript_info_file" format="tabular" metadata_source="gtf_file" label="${tool.name} on ${on_string}: Table"> |
| 67 <filter>advanced_options['infoOut']</filter> | 67 <filter>(advanced_options['advanced_options_selector'] == 'advanced') and (advanced_options['infoOut'])</filter> |
| 68 </data> | 68 </data> |
| 69 </outputs> | 69 </outputs> |
| 70 <tests> | 70 <tests> |
| 71 <test> | 71 <test expect_num_outputs="1" > |
| 72 <param name="gtf_file" value="gtf2bed_test.gtf"/> | 72 <param name="gtf_file" value="gtf2bed_test.gtf"/> |
| 73 <output name="bed_file" file="gtf2bed_test.bed" ftype="bed12"/> | 73 <output name="bed_file" file="gtf2bed_test.bed" ftype="bed12"/> |
| 74 </test> | 74 </test> |
| 75 <test> | 75 <test expect_num_outputs="1" > |
| 76 <param name="gtf_file" value="gtf2bed_test_missing_exon.gtf"/> | 76 <param name="gtf_file" value="gtf2bed_test_missing_exon.gtf"/> |
| 77 <param name="advanced_options_selector" value="advanced" /> | 77 <param name="advanced_options_selector" value="advanced" /> |
| 78 <param name="ignoreGroupsWithoutExons" value="true" /> | 78 <param name="ignoreGroupsWithoutExons" value="true" /> |
| 79 <output name="bed_file" file="gtf2bed_test_missing_exon.bed" ftype="bed12"/> | 79 <output name="bed_file" file="gtf2bed_test_missing_exon.bed" ftype="bed12"/> |
| 80 </test> | 80 </test> |
| 81 <test> | 81 <test expect_num_outputs="1" > |
| 82 <param name="gtf_file" value="gtf2bed_test.gtf"/> | 82 <param name="gtf_file" value="gtf2bed_test.gtf"/> |
| 83 <param name="advanced_options_selector" value="advanced" /> | 83 <param name="advanced_options_selector" value="advanced" /> |
| 84 <param name="includeVersion" value="true" /> | 84 <param name="includeVersion" value="true" /> |
| 85 <output name="bed_file" file="gtf2bed_test_include_version.bed" ftype="bed12"/> | 85 <output name="bed_file" file="gtf2bed_test_include_version.bed" ftype="bed12"/> |
| 86 </test> | 86 </test> |
| 87 <test> | 87 <test expect_num_outputs="2" > |
| 88 <param name="gtf_file" value="gtf2bed_test.gtf"/> | 88 <param name="gtf_file" value="gtf2bed_test.gtf"/> |
| 89 <param name="advanced_options_selector" value="advanced" /> | 89 <param name="advanced_options_selector" value="advanced" /> |
| 90 <param name="infoOut" value="true" /> | 90 <param name="infoOut" value="true" /> |
| 91 <output name="bed_file" file="gtf2bed_test.bed" ftype="bed12"/> | 91 <output name="bed_file" file="gtf2bed_test.bed" ftype="bed12"/> |
| 92 <output name="transcript_info_file" file="gtf2bed_test_transcript_info.txt" ftype="tabular"/> | 92 <output name="transcript_info_file" file="gtf2bed_test_transcript_info.txt" ftype="tabular"/> |
| 93 </test> | 93 </test> |
| 94 <test> | 94 <test expect_num_outputs="1" > |
| 95 <param name="gtf_file" value="gtf2bed_test.gtf"/> | 95 <param name="gtf_file" value="gtf2bed_test.gtf"/> |
| 96 <param name="advanced_options_selector" value="advanced" /> | 96 <param name="advanced_options_selector" value="advanced" /> |
| 97 <repeat name="sourcePrefixes"> | 97 <repeat name="sourcePrefixes"> |
| 98 <param name="sourcePrefix" value="hav" /> | 98 <param name="sourcePrefix" value="hav" /> |
| 99 </repeat> | 99 </repeat> |
| 100 <output name="bed_file" file="gtf2bed_test_havana.bed" ftype="bed12"/> | 100 <output name="bed_file" file="gtf2bed_test_havana.bed" ftype="bed12"/> |
| 101 </test> | 101 </test> |
| 102 <test> | 102 <test expect_num_outputs="1" > |
| 103 <param name="gtf_file" value="gtf2bed_test.gtf"/> | 103 <param name="gtf_file" value="gtf2bed_test.gtf"/> |
| 104 <param name="advanced_options_selector" value="advanced" /> | 104 <param name="advanced_options_selector" value="advanced" /> |
| 105 <repeat name="sourcePrefixes"> | 105 <repeat name="sourcePrefixes"> |
| 106 <param name="sourcePrefix" value="hav" /> | 106 <param name="sourcePrefix" value="hav" /> |
| 107 </repeat> | 107 </repeat> |