| Previous changeset 6:b5527cc104ab (2022-08-15) Next changeset 8:a389f74c3630 (2023-11-20) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit deb37086489259607f5edcba25750434bbf4823e |
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modified:
samtools_markdup.xml |
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| diff -r b5527cc104ab -r ce32171c6d44 samtools_markdup.xml --- a/samtools_markdup.xml Mon Aug 15 09:17:57 2022 +0000 +++ b/samtools_markdup.xml Fri Apr 07 21:47:07 2023 +0000 |
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| @@ -1,4 +1,4 @@ -<tool id="samtools_markdup" name="Samtools markdup" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@" > +<tool id="samtools_markdup" name="Samtools markdup" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@" > <description>marks duplicate alignments</description> <macros> <import>macros.xml</import> @@ -85,9 +85,9 @@ <!-- output bam, if input was name sorted then restore this sorting order --> <data name="output" format="bam" from_work_dir="outfile" label="${tool.name} on ${on_string}"> <change_format> - <when input="output_format.select_oformat" value="SAM" format="sam" /> - <when input="output_format.select_oformat" value="BAM" format="bam" /> - <when input="output_format.select_oformat" value="CRAM" format="cram" /> + <when input="output_options.output_format.select_oformat" value="SAM" format="sam" /> + <when input="output_options.output_format.select_oformat" value="BAM" format="bam" /> + <when input="output_options.output_format.select_oformat" value="CRAM" format="cram" /> </change_format> </data> <data name="stats_output" format="txt" label="${tool.name} on ${on_string}: statistics"> @@ -97,31 +97,31 @@ <tests> <!-- 1) --> <test expect_num_outputs="1"> - <param name="bamfile" value="1_markdup.sam" /> + <param name="bamfile" value="1_markdup.sam" ftype="sam" /> <output name="output" file="1_markdup.expected.bam" ftype="bam" lines_diff="4" /> </test> <!-- 2) --> <test expect_num_outputs="1"> - <param name="bamfile" value="2_remove_dups.sam" /> + <param name="bamfile" value="2_remove_dups.sam" ftype="sam" /> <param name="remove" value="-r" /> <output name="output" file="2_remove_dups.expected.bam" ftype="bam" lines_diff="4" /> </test> <!-- 3) --> <test expect_num_outputs="1"> - <param name="bamfile" value="3_mark_supp_dup.bam" /> + <param name="bamfile" value="3_mark_supp_dup.bam" ftype="bam" /> <param name="supp" value="-S" /> <output name="output" file="3_mark_supp_dup.expected.bam" ftype="bam" lines_diff="4" /> </test> <!-- 4) test stats output --> <test expect_num_outputs="2"> - <param name="bamfile" value="1_markdup.sam" /> + <param name="bamfile" value="1_markdup.sam" ftype="sam"/> <param name="stats" value="yes" /> <output name="output" file="1_markdup.expected.bam" ftype="bam" lines_diff="4" /> <output name="stats_output" file="stats.txt" lines_diff="2" /> </test> <!-- 5) check that stderr is not swallowed w test data from fixmate --> <test expect_num_outputs="2" expect_exit_code="1" expect_failure="true"> - <param name="bamfile" value="3_two_read_mapped.sam" /> + <param name="bamfile" value="3_two_read_mapped.sam" ftype="sam" /> <param name="stats" value="yes"/> <!-- for some reason this is not possible at the moment <output name="stats_output"> @@ -135,35 +135,35 @@ </test> <!-- 6) check optical distance and check -c option --> <test expect_num_outputs="1"> - <param name="bamfile" value="1_markdup.sam" /> + <param name="bamfile" value="1_markdup.sam" ftype="sam"/> <param name="odist" value="10" /> <param name="existing_tags" value="-c" /> <output name="output" file="6_markdup.expected.bam" ftype="bam" lines_diff="4" /> </test> <!-- 7) check new mode s --> <test expect_num_outputs="1"> - <param name="bamfile" value="1_markdup.sam" /> + <param name="bamfile" value="1_markdup.sam" ftype="sam"/> <param name="mode" value="s" /> <output name="output" file="7_markdup.expected.bam" ftype="bam" lines_diff="4" /> </test> <!-- 8) check include-fails --> <test expect_num_outputs="1"> - <param name="bamfile" value="1_markdup.sam" /> + <param name="bamfile" value="1_markdup.sam" ftype="sam"/> <param name="include_fails" value="true" /> <output name="output" file="8_markdup.expected.bam" ftype="bam" lines_diff="4" /> </test> <!-- 9) test sam format --> <test expect_num_outputs="1"> - <param name="bamfile" value="1_markdup.sam" /> + <param name="bamfile" value="1_markdup.sam" ftype="sam"/> <param name="select_oformat" value="SAM" /> - <output name="output" file="9_markdup.expected.sam" lines_diff="4" /> + <output name="output" file="9_markdup.expected.sam" ftype="sam" lines_diff="4" /> </test> <!-- 10) test cram format --> <test expect_num_outputs="1"> - <param name="bamfile" value="10_markdup.sam" /> + <param name="bamfile" value="10_markdup.sam" ftype="sam"/> <param name="select_oformat" value="CRAM" /> <param name="ref_file" value="test.fa" /> - <output name="output" file="10_markdup.expected.cram" compare="sim_size" delta="250"/> + <output name="output" file="10_markdup.expected.cram" ftype="cram" compare="sim_size" delta="250"/> </test> </tests> <help> |