Mercurial > repos > bgruening > gfastats
changeset 2:ad1149b4f795 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 0c9612e0257a872892894530669785d1e02aaacc
| author | bgruening |
|---|---|
| date | Wed, 01 Jun 2022 15:15:57 +0000 |
| parents | 2b8b4cacb83d |
| children | 8ccbf07a5433 |
| files | gfastats.xml macros.xml test-data/regions.bed test-data/test_11_stats.tabular |
| diffstat | 4 files changed, 100 insertions(+), 2 deletions(-) [+] |
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--- a/gfastats.xml Mon Apr 25 09:38:18 2022 +0000 +++ b/gfastats.xml Wed Jun 01 15:15:57 2022 +0000 @@ -75,7 +75,7 @@ </param> <when value="false"/> <when value="true"> - <param name="target_sequence" type="text" value="" label="Target sequence" help="Target specific sequence by header, optionally with coordinates: header[:start-end]"> + <param name="target_sequence" type="text" value="" label="Target sequence" optional="true" help="Target specific sequence by header, optionally with coordinates: header[:start-end]"> <sanitizer invalid_char=""> <valid initial="string.digits,string.letters"> <add value=":"/> @@ -325,6 +325,15 @@ </conditional> <output name="output" value="test_10.gfa" ftype="gfa1"/> </test> + <!--Test 11 --> + <test expect_num_outputs="1"> + <param name="input_file" value="dataset_03.fasta"/> + <conditional name="target_condition"> + <param name="target_option" value="true"/> + <param name="include_bed" value="regions.bed"/> + </conditional> + <output name="stats" value="test_11_stats.tabular" ftype="tabular"/> + </test> </tests> <help><![CDATA[
--- a/macros.xml Mon Apr 25 09:38:18 2022 +0000 +++ b/macros.xml Wed Jun 01 15:15:57 2022 +0000 @@ -1,5 +1,5 @@ <macros> - <token name="@TOOL_VERSION@">1.2.1</token> + <token name="@TOOL_VERSION@">1.2.2</token> <token name="@SUFFIX_VERSION@">0</token> <xml name="requirements"> <requirements>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/regions.bed Wed Jun 01 15:15:57 2022 +0000 @@ -0,0 +1,1 @@ +contig_1 0 1680
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_11_stats.tabular Wed Jun 01 15:15:57 2022 +0000 @@ -0,0 +1,88 @@ +# scaffolds 1 +Total scaffold length 1680 +Average scaffold length 1680.00 +Scaffold N50 1680 +Scaffold auN 1680.00 +Scaffold L50 1 +Largest scaffold 1680 +Total contig length 1679 +Average contig length 839.50 +Contig N50 922 +Contig auN 847.61 +Contig L50 1 +Largest contig 922 +# gaps in scaffolds 1 +Total gap length in scaffolds 1 +Average gap length in scaffolds 1.00 +Gap N50 in scaffolds 1 +Gap auN in scaffolds 1.00 +Gap L50 in scaffolds 1 +Largest gap in scaffolds 1 +Base composition (A:C:G:T) 388:497:402:392 +GC content % 53.54 +# soft-masked bases 0 +# segments 2 +Total segment length 1679 +Average segment length 839.50 +# gaps 1 +# paths 1 +Scaffold N10 1680 +Scaffold N20 1680 +Scaffold N30 1680 +Scaffold N40 1680 +Scaffold N50 1680 +Scaffold N60 1680 +Scaffold N70 1680 +Scaffold N80 1680 +Scaffold N90 1680 +Scaffold N100 1680 +Scaffold L10 1 +Scaffold L20 1 +Scaffold L30 1 +Scaffold L40 1 +Scaffold L50 1 +Scaffold L60 1 +Scaffold L70 1 +Scaffold L80 1 +Scaffold L90 1 +Scaffold L100 1 +Contig N10 922 +Contig N20 922 +Contig N30 922 +Contig N40 922 +Contig N50 922 +Contig N60 757 +Contig N70 757 +Contig N80 757 +Contig N90 757 +Contig N100 757 +Contig L10 1 +Contig L20 1 +Contig L30 1 +Contig L40 1 +Contig L50 1 +Contig L60 2 +Contig L70 2 +Contig L80 2 +Contig L90 2 +Contig L100 2 +Gap N10 1 +Gap N20 1 +Gap N30 1 +Gap N40 1 +Gap N50 1 +Gap N60 1 +Gap N70 1 +Gap N80 1 +Gap N90 1 +Gap N100 1 +Gap L10 1 +Gap L20 1 +Gap L30 1 +Gap L40 1 +Gap L50 1 +Gap L60 1 +Gap L70 1 +Gap L80 1 +Gap L90 1 +Gap L100 1