Mercurial > repos > iuc > seqkit_fx2tab
changeset 11:b91a71153b2f draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 10a55aa92dba7af64cfa0a308191722655a9fba9
| author | iuc |
|---|---|
| date | Tue, 19 Aug 2025 17:14:34 +0000 |
| parents | 654a2f089252 |
| children | bfeec7371833 |
| files | macros.xml seqkit_fx2tab.xml test-data/fx2tab_output4.tabular |
| diffstat | 3 files changed, 27 insertions(+), 5 deletions(-) [+] |
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--- a/macros.xml Tue Jul 15 19:35:45 2025 +0000 +++ b/macros.xml Tue Aug 19 17:14:34 2025 +0000 @@ -1,6 +1,6 @@ <macros> <token name="@TOOL_VERSION@">2.10.0</token> - <token name="@VERSION_SUFFIX@">1</token> + <token name="@VERSION_SUFFIX@">2</token> <token name="@PROFILE@">24.0</token> <xml name="bio_tools"> <xrefs>
--- a/seqkit_fx2tab.xml Tue Jul 15 19:35:45 2025 +0000 +++ b/seqkit_fx2tab.xml Tue Aug 19 17:14:34 2025 +0000 @@ -15,6 +15,12 @@ '${input_identifier}' $alphabet $avg_qual +#if str($B) != 'None' + -B ${ str($B).replace(",","") } +#end if +#if str($C) != 'None' + -C ${ str($C).replace(",","") } +#end if $gc $gc_skew $header_line @@ -32,6 +38,20 @@ <param name="input" type="data" format="fasta,fasta.gz,fastqsanger,fastqsanger.gz" label="Input file"/> <param argument="--alphabet" type="boolean" truevalue="--alphabet" falsevalue="" checked="false" label="Output alphabet letters?"/> <param argument="--avg_qual" type="boolean" truevalue="--avg-qual" falsevalue="" checked="false" label="Output average quality of the read?"/> + <param argument="-B" type="select" multiple="true" label="Append a precentage column of the selected bases"> + <option value="A"></option> + <option value="G"></option> + <option value="C"></option> + <option value="T"></option> + <option value="N"></option> + </param> + <param argument="-C" type="select" multiple="true" label="Append a count column of the selected bases"> + <option value="A"></option> + <option value="G"></option> + <option value="C"></option> + <option value="T"></option> + <option value="N"></option> + </param> <param argument="--gc" type="boolean" truevalue="--gc" falsevalue="" checked="false" label="Output GC content?"/> <param argument="--gc_skew" type="boolean" truevalue="--gc-skew" falsevalue="" checked="false" label="Output GC-Skew?"/> <param argument="--header_line" type="boolean" truevalue="--header-line" falsevalue="" checked="false" label="Output header line?"/> @@ -66,6 +86,8 @@ <param name="input" value="input1.fasta.gz" ftype="fasta.gz"/> <param name="alphabet" value="true"/> <param name="avg_qual" value="true"/> + <param name="B" value="A,T"/> + <param name="C" value="A"/> <param name="gc" value="true"/> <param name="gc_skew" value="true"/> <param name="header_line" value="true"/>
--- a/test-data/fx2tab_output4.tabular Tue Jul 15 19:35:45 2025 +0000 +++ b/test-data/fx2tab_output4.tabular Tue Aug 19 17:14:34 2025 +0000 @@ -1,4 +1,4 @@ -#id length GC GC-Skew alphabet avg.qual seq.hash -ENA|AB011145|AB011145.1 4796 38.47 11.65 ACGT 0.00 c19cf05cadbdbc26e22efc2201acfcec -ENA|M10051|M10051.1 4723 55.24 0.50 ACGT 0.00 4f6bbf79e427ef90b6f31de5023ad241 -ENA|BC112106|BC112106.1 1213 58.78 -15.01 ACGT 0.00 3b099f7df389373bb7e3269efc819599 +#id length GC GC-Skew A AT alphabet avg.qual seq.hash +ENA|AB011145|AB011145.1 4796 38.47 11.65 1545 61.53 ACGT 0.00 c19cf05cadbdbc26e22efc2201acfcec +ENA|M10051|M10051.1 4723 55.24 0.50 1068 44.76 ACGT 0.00 4f6bbf79e427ef90b6f31de5023ad241 +ENA|BC112106|BC112106.1 1213 58.78 -15.01 233 41.22 ACGT 0.00 3b099f7df389373bb7e3269efc819599