Mercurial > repos > iuc > seqkit_fx2tab

comparison seqkit_fx2tab.xml @ 11:b91a71153b2f draft

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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
comparison
equal deleted inserted replaced
10:654a2f089252 11:b91a71153b2f
13 13
14 seqkit fx2tab 14 seqkit fx2tab
15 '${input_identifier}' 15 '${input_identifier}'
16 $alphabet 16 $alphabet
17 $avg_qual 17 $avg_qual
18 #if str($B) != 'None'
19 -B ${ str($B).replace(",","") }
20 #end if
21 #if str($C) != 'None'
22 -C ${ str($C).replace(",","") }
23 #end if
18 $gc 24 $gc
19 $gc_skew 25 $gc_skew
20 $header_line 26 $header_line
21 $length 27 $length
22 $name 28 $name
30 ]]></command> 36 ]]></command>
31 <inputs> 37 <inputs>
32 <param name="input" type="data" format="fasta,fasta.gz,fastqsanger,fastqsanger.gz" label="Input file"/> 38 <param name="input" type="data" format="fasta,fasta.gz,fastqsanger,fastqsanger.gz" label="Input file"/>
33 <param argument="--alphabet" type="boolean" truevalue="--alphabet" falsevalue="" checked="false" label="Output alphabet letters?"/> 39 <param argument="--alphabet" type="boolean" truevalue="--alphabet" falsevalue="" checked="false" label="Output alphabet letters?"/>
34 <param argument="--avg_qual" type="boolean" truevalue="--avg-qual" falsevalue="" checked="false" label="Output average quality of the read?"/> 40 <param argument="--avg_qual" type="boolean" truevalue="--avg-qual" falsevalue="" checked="false" label="Output average quality of the read?"/>
41 <param argument="-B" type="select" multiple="true" label="Append a precentage column of the selected bases">
42 <option value="A"></option>
43 <option value="G"></option>
44 <option value="C"></option>
45 <option value="T"></option>
46 <option value="N"></option>
47 </param>
48 <param argument="-C" type="select" multiple="true" label="Append a count column of the selected bases">
49 <option value="A"></option>
50 <option value="G"></option>
51 <option value="C"></option>
52 <option value="T"></option>
53 <option value="N"></option>
54 </param>
35 <param argument="--gc" type="boolean" truevalue="--gc" falsevalue="" checked="false" label="Output GC content?"/> 55 <param argument="--gc" type="boolean" truevalue="--gc" falsevalue="" checked="false" label="Output GC content?"/>
36 <param argument="--gc_skew" type="boolean" truevalue="--gc-skew" falsevalue="" checked="false" label="Output GC-Skew?"/> 56 <param argument="--gc_skew" type="boolean" truevalue="--gc-skew" falsevalue="" checked="false" label="Output GC-Skew?"/>
37 <param argument="--header_line" type="boolean" truevalue="--header-line" falsevalue="" checked="false" label="Output header line?"/> 57 <param argument="--header_line" type="boolean" truevalue="--header-line" falsevalue="" checked="false" label="Output header line?"/>
38 <param argument="--length" type="boolean" truevalue="--length" falsevalue="" checked="false" label="Output sequence length?"/> 58 <param argument="--length" type="boolean" truevalue="--length" falsevalue="" checked="false" label="Output sequence length?"/>
39 <param argument="--name" type="boolean" truevalue="--name" falsevalue="" checked="false" label="Output only names (no sequences and qualities)?"/> 59 <param argument="--name" type="boolean" truevalue="--name" falsevalue="" checked="false" label="Output only names (no sequences and qualities)?"/>
64 </test> 84 </test>
65 <test expect_num_outputs="1"> 85 <test expect_num_outputs="1">
66 <param name="input" value="input1.fasta.gz" ftype="fasta.gz"/> 86 <param name="input" value="input1.fasta.gz" ftype="fasta.gz"/>
67 <param name="alphabet" value="true"/> 87 <param name="alphabet" value="true"/>
68 <param name="avg_qual" value="true"/> 88 <param name="avg_qual" value="true"/>
89 <param name="B" value="A,T"/>
90 <param name="C" value="A"/>
69 <param name="gc" value="true"/> 91 <param name="gc" value="true"/>
70 <param name="gc_skew" value="true"/> 92 <param name="gc_skew" value="true"/>
71 <param name="header_line" value="true"/> 93 <param name="header_line" value="true"/>
72 <param name="length" value="true"/> 94 <param name="length" value="true"/>
73 <param name="name" value="true"/> 95 <param name="name" value="true"/>