Mercurial > repos > iuc > seqkit_fx2tab
diff seqkit_fx2tab.xml @ 7:6f3db0c7a725 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
| author | iuc |
|---|---|
| date | Fri, 26 Sep 2025 16:47:22 +0000 |
| parents | 8d9ee1d00f7f |
| children |
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--- a/seqkit_fx2tab.xml Mon Mar 17 09:50:29 2025 +0000 +++ b/seqkit_fx2tab.xml Fri Sep 26 16:47:22 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?"/> @@ -51,11 +71,11 @@ </test> <test expect_num_outputs="1"> <param name="input" value="input1.fastq.gz" ftype="fastqsanger.gz"/> - <param name="avg_qual" value="--avg-qual"/> - <param name="header_line" value="--header-line"/> - <param name="length" value="--length"/> - <param name="name" value="--name"/> - <param name="only_id" value="--only-id"/> + <param name="avg_qual" value="true"/> + <param name="header_line" value="true"/> + <param name="length" value="true"/> + <param name="name" value="true"/> + <param name="only_id" value="true"/> <output name="output" file="fx2tab_output2.tabular" ftype="tabular"/> </test> <test expect_num_outputs="1"> @@ -64,16 +84,18 @@ </test> <test expect_num_outputs="1"> <param name="input" value="input1.fasta.gz" ftype="fasta.gz"/> - <param name="alphabet" value="--alphabet"/> - <param name="avg_qual" value="--avg-qual"/> - <param name="gc" value="--gc"/> - <param name="gc_skew" value="--gc-skew"/> - <param name="header_line" value="--header-line"/> - <param name="length" value="--length"/> - <param name="name" value="--name"/> - <param name="no_qual" value="--no-qual"/> - <param name="only_id" value="--only-id"/> - <param name="seq_hash" value="--seq-hash"/> + <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"/> + <param name="length" value="true"/> + <param name="name" value="true"/> + <param name="no_qual" value="true"/> + <param name="only_id" value="true"/> + <param name="seq_hash" value="true"/> <output name="output" file="fx2tab_output4.tabular" ftype="tabular"/> </test> </tests>