| Previous changeset 9:40fa6c240105 (2024-09-08) Next changeset 11:56fb540810ce (2025-11-12) |
|
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit c508c3af0f4121dcc38e0be63db00a604e997b8a |
|
modified:
macros.xml samtools_markdup.xml |
| b |
| diff -r 40fa6c240105 -r 229ba92a3b55 macros.xml --- a/macros.xml Sun Sep 08 03:26:14 2024 +0000 +++ b/macros.xml Thu Jun 19 13:00:18 2025 +0000 |
| [ |
| @@ -11,8 +11,8 @@ please only bump the minor version in order to let the requirement version catch up eventually). To find the tools check: `grep "<tool" . -r | grep -v VERSION_SUFFIX | cut -d":" -f 1` --> - <token name="@TOOL_VERSION@">1.20</token> - <token name="@VERSION_SUFFIX@">2</token> + <token name="@TOOL_VERSION@">1.21</token> + <token name="@VERSION_SUFFIX@">0</token> <token name="@PROFILE@">22.05</token> <token name="@FLAGS@"><![CDATA[ #set $flags = 0 @@ -220,6 +220,7 @@ <xml name="citations"> <citations> <citation type="doi">10.1093/gigascience/giab008</citation> + <citation type="doi">10.1093/bioinformatics/btr076</citation> </citations> </xml> <xml name="version_command"> |
| b |
| diff -r 40fa6c240105 -r 229ba92a3b55 samtools_markdup.xml --- a/samtools_markdup.xml Sun Sep 08 03:26:14 2024 +0000 +++ b/samtools_markdup.xml Thu Jun 19 13:00:18 2025 +0000 |
| b |
| @@ -103,13 +103,13 @@ <!-- 2) --> <test expect_num_outputs="1"> <param name="bamfile" value="2_remove_dups.sam" ftype="sam" /> - <param name="remove" value="-r" /> + <param name="remove" value="true" /> <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" ftype="bam" /> - <param name="supp" value="-S" /> + <param name="supp" value="true" /> <output name="output" file="3_mark_supp_dup.expected.bam" ftype="bam" lines_diff="4" /> <assert_command> <has_text text="samtools sort" negate="true"/> @@ -118,14 +118,18 @@ <!-- 4) test stats output --> <test expect_num_outputs="2"> <param name="bamfile" value="1_markdup.sam" ftype="sam"/> - <param name="stats" value="yes" /> + <section name="output_options"> + <param name="stats" value="yes" /> + </section> <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_exit_code="1" expect_failure="true"> <param name="bamfile" value="3_two_read_mapped.sam" ftype="sam" /> - <param name="stats" value="yes"/> + <section name="output_options"> + <param name="stats" value="yes"/> + </section> <assert_stderr> <has_line line="samtools markdup: error, no MC tag. Please run samtools fixmate on file first."/> <has_line line="samtools markdup: error, unable to assign pair hash key."/> @@ -135,7 +139,7 @@ <test expect_num_outputs="1"> <param name="bamfile" value="1_markdup.sam" ftype="sam"/> <param name="odist" value="10" /> - <param name="existing_tags" value="-c" /> + <param name="existing_tags" value="true" /> <output name="output" file="6_markdup.expected.bam" ftype="bam" lines_diff="4" /> </test> <!-- 7) check new mode s --> @@ -153,7 +157,11 @@ <!-- 9) test sam format --> <test expect_num_outputs="1"> <param name="bamfile" value="1_markdup.sam" ftype="sam"/> - <param name="select_oformat" value="SAM" /> + <section name="output_options"> + <conditional name="output_format"> + <param name="select_oformat" value="SAM" /> + </conditional> + </section> <output name="output" file="9_markdup.expected.sam" ftype="sam" lines_diff="4" /> </test> <!-- 10) essentially the same as test 9 (just converted input to sorted bam .. but telling Galaxy its qname sorted) @@ -161,7 +169,11 @@ ie. the qname_sorted bam is not converted implicitly --> <test expect_num_outputs="1"> <param name="bamfile" value="1_markdup.qname_sorted.bam" ftype="qname_sorted.bam" /> - <param name="select_oformat" value="SAM" /> + <section name="output_options"> + <conditional name="output_format"> + <param name="select_oformat" value="SAM" /> + </conditional> + </section> <output name="output" file="9_markdup.expected.sam" lines_diff="4" /> <assert_command> <has_text text="samtools sort"/> @@ -171,8 +183,12 @@ <!-- 11) test cram format --> <test expect_num_outputs="1"> <param name="bamfile" value="10_markdup.sam" ftype="sam"/> - <param name="select_oformat" value="CRAM" /> - <param name="ref_file" value="test.fa" /> + <section name="output_options"> + <conditional name="output_format"> + <param name="select_oformat" value="CRAM" /> + <param name="ref_file" value="test.fa" /> + </conditional> + </section> <output name="output" file="11_markdup.expected.cram" ftype="cram" compare="sim_size" delta="250"/> <assert_command> <has_text text="samtools sort"/> |