Mercurial > repos > iuc > seqkit_fx2tab

comparison seqkit_fx2tab.xml @ 7:6f3db0c7a725 draft

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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
comparison
equal deleted inserted replaced
6:8eed2ffb2f6a 7:6f3db0c7a725
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)?"/>
49 <param name="input" value="input1.fastq.gz" ftype="fastqsanger.gz"/> 69 <param name="input" value="input1.fastq.gz" ftype="fastqsanger.gz"/>
50 <output name="output" file="fx2tab_output1.tabular" ftype="tabular"/> 70 <output name="output" file="fx2tab_output1.tabular" ftype="tabular"/>
51 </test> 71 </test>
52 <test expect_num_outputs="1"> 72 <test expect_num_outputs="1">
53 <param name="input" value="input1.fastq.gz" ftype="fastqsanger.gz"/> 73 <param name="input" value="input1.fastq.gz" ftype="fastqsanger.gz"/>
54 <param name="avg_qual" value="--avg-qual"/> 74 <param name="avg_qual" value="true"/>
55 <param name="header_line" value="--header-line"/> 75 <param name="header_line" value="true"/>
56 <param name="length" value="--length"/> 76 <param name="length" value="true"/>
57 <param name="name" value="--name"/> 77 <param name="name" value="true"/>
58 <param name="only_id" value="--only-id"/> 78 <param name="only_id" value="true"/>
59 <output name="output" file="fx2tab_output2.tabular" ftype="tabular"/> 79 <output name="output" file="fx2tab_output2.tabular" ftype="tabular"/>
60 </test> 80 </test>
61 <test expect_num_outputs="1"> 81 <test expect_num_outputs="1">
62 <param name="input" value="input1.fasta.gz" ftype="fasta.gz"/> 82 <param name="input" value="input1.fasta.gz" ftype="fasta.gz"/>
63 <output name="output" file="fx2tab_output3.tabular" ftype="tabular"/> 83 <output name="output" file="fx2tab_output3.tabular" ftype="tabular"/>
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="--alphabet"/> 87 <param name="alphabet" value="true"/>
68 <param name="avg_qual" value="--avg-qual"/> 88 <param name="avg_qual" value="true"/>
69 <param name="gc" value="--gc"/> 89 <param name="B" value="A,T"/>
70 <param name="gc_skew" value="--gc-skew"/> 90 <param name="C" value="A"/>
71 <param name="header_line" value="--header-line"/> 91 <param name="gc" value="true"/>
72 <param name="length" value="--length"/> 92 <param name="gc_skew" value="true"/>
73 <param name="name" value="--name"/> 93 <param name="header_line" value="true"/>
74 <param name="no_qual" value="--no-qual"/> 94 <param name="length" value="true"/>
75 <param name="only_id" value="--only-id"/> 95 <param name="name" value="true"/>
76 <param name="seq_hash" value="--seq-hash"/> 96 <param name="no_qual" value="true"/>
97 <param name="only_id" value="true"/>
98 <param name="seq_hash" value="true"/>
77 <output name="output" file="fx2tab_output4.tabular" ftype="tabular"/> 99 <output name="output" file="fx2tab_output4.tabular" ftype="tabular"/>
78 </test> 100 </test>
79 </tests> 101 </tests>
80 <help> 102 <help>
81 **What it does** 103 **What it does**