Mercurial > repos > bgruening > diamond
diff diamond_view.xml @ 20:0729ae1533e5 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 62db819c1db857d3fba94dc4e290ee0f50f7928d
| author | iuc |
|---|---|
| date | Mon, 03 Feb 2025 16:00:43 +0000 |
| parents | 7ff284249149 |
| children |
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--- a/diamond_view.xml Fri Apr 22 13:50:54 2022 +0000 +++ b/diamond_view.xml Mon Feb 03 16:00:43 2025 +0000 @@ -1,11 +1,11 @@ -<tool id="bg_diamond_view" name="Diamond view" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="19.01"> +<tool id="bg_diamond_view" name="Diamond view" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.2" license="GPL-3.0"> <description>generate formatted output from DAA files</description> <macros> <import>macros.xml</import> </macros> - <expand macro="requirements" /> - <expand macro="stdio" /> - <expand macro="version_command" /> + <expand macro="requirements"/> + <expand macro="stdio"/> + <expand macro="version_command"/> <command detect_errors="aggressive"><![CDATA[ ## need to link because diamont tries to open dataset_xxx.dat.daa ln -s '$daa' input.daa && @@ -16,23 +16,23 @@ @OUTPUT_ARGS@ @HITFILTER_ARGS@ $forwardonly - --compress '0' + --verbose ]]> </command> <inputs> - <param argument="--daa" type="data" format="daa" label="input file in DAA format" /> + <param argument="--daa" type="data" format="daa" label="input file in DAA format"/> <section name="output_section" title="Output options"> - <expand macro="output_type_macro" /> + <expand macro="output_type_macro"/> </section> - <expand macro="hit_filter_macro" /> - <param argument="--forwardonly" type="boolean" truevalue="--forwardonly" falsevalue="" checked="false" label="only show alignments of forward strand" help=""/> + <expand macro="hit_filter_macro"/> + <param argument="--forwardonly" type="boolean" truevalue="--forwardonly" falsevalue="" checked="false" label="only show alignments of forward strand"/> </inputs> <outputs> - <expand macro="output_macro" /> + <expand macro="output_macro"/> </outputs> <tests> <test expect_num_outputs="1"> - <param name="daa" ftype="daa" value="diamond_results.daa" /> + <param name="daa" ftype="daa" value="diamond_results.daa"/> <section name="output_section"> <conditional name="output"> <param name="outfmt" value="5"/> @@ -40,12 +40,12 @@ </section> <conditional name="hit_filter"> <param name="hit_filter_select" value="max"/> - <param name="max_target_seqs" value="1" /> + <param name="max_target_seqs" value="1"/> </conditional> <output name="blast_tabular" file="diamond_results.xml"/> </test> <test expect_num_outputs="1"> - <param name="daa" ftype="daa" value="diamond_results.daa" /> + <param name="daa" ftype="daa" value="diamond_results.daa"/> <section name="output_section"> <conditional name="output"> <param name="outfmt" value="6"/> @@ -55,7 +55,7 @@ <output name="blast_tabular" file="diamond_view_results.tabular"/> </test> <test expect_num_outputs="1"> - <param name="daa" ftype="daa" value="diamond_results.daa" /> + <param name="daa" ftype="daa" value="diamond_results.daa"/> <section name="output_section"> <conditional name="output"> <param name="outfmt" value="101"/> @@ -63,13 +63,12 @@ </section> <conditional name="hit_filter"> <param name="hit_filter_select" value="top"/> - <param name="max_target_seqs" value="1" /> + <param name="max_target_seqs" value="1"/> </conditional> - <param name="forwardonly" value="--forwardonly" /> + <param name="forwardonly" value="--forwardonly"/> <output name="blast_tabular" file="diamond_results.sam" lines_diff="2"/> </test> </tests> - <help> <![CDATA[ @@ -103,5 +102,5 @@ 12 Bit score ]]> </help> - <expand macro="citations" /> + <expand macro="citations"/> </tool>