ktoolu/kt_combine.xml at master · cschu/ktoolu · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
<tool id="kt_combine" name="ktoolu combine" version="0.1.0">
    <description>Combine results from two different kraken runs.</description>
    <requirements>
        <requirement type="package" version="2.7">python</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" />
    </stdio>

    <command interpreter="python"><![CDATA[
        kt_combine.py
         --kraken-resultsA "${krakenA}"
         --kraken-resultsB "${krakenB}"
         --inR1 "${inputData.inputR1}"
         --outAR1 "${outputAR1}"
         --outBR1 "${outputBR1}"
         --outABR1 "${outputABR1}"
         --outUR1 "${outputUR1}"

         #if $inputData.inputFormat == "pairedFastq" or $inputData.inputFormat == "pairedFasta":
          --inR2 "${inputData.inputR2}"
          --outAR2 "${outputAR2}"
          --outBR2 "${outputBR2}"
          --outABR2 "${outputABR2}"
          --outUR2 "${outputUR2}"
        #end if

        #if $inputData.inputFormat == "singleFastq" or $inputData.inputFormat == "pairedFastq":
          --input-format "fq"
        #else:
          --input-format "fa"
        #end if
        > "${combineSummary}"
    ]]></command>
    <inputs>
      <param name="krakenA" type="data" format="tabular" label="Kraken classification output set A" />
		  <param name="krakenB" type="data" format="tabular" label="Kraken classification output set B" />

      <conditional name="inputData">
        <param name="inputFormat" type="select" label="Please select input file type and library type.">
          <option value="singleFastq">Single-end Fastq</option>
				  <option value="pairedFastq">Paired-end Fastq</option>
          <option value="singleFasta">Single-end Fasta</option>
          <option value="pairedFasta">Paired-end Fasta</option>
        </param>
        <when value="singleFastq">
          <param name="inputR1" type="data" format="fastq,fq,fastqsanger,fastqsolexa,fastqillumina,fastq.gz,fq.gz,fastq.bz2,fq.bz2" label="Forward/single end (R1) Fastq file" />
        </when>
        <when value="pairedFastq">
          <param name="inputR1" type="data" format="fastq,fq,fastqsanger,fastqsolexa,fastqillumina,fastq.gz,fq.gz,fastq.bz2,fq.bz2" label="Forward/single end (R1) Fastq file" />
          <param name="inputR2" type="data" format="fastq,fq,fastqsanger,fastqsolexa,fastqillumina,fastq.gz,fq.gz,fastq.bz2,fq.bz2" label="Reverse (R2) Fastq file" />
        </when>
        <when value="singleFasta">
          <param name="inputR1" type="data" format="fasta,fa,fas,fasta.gz,fa.gz,fas.gz,fasta.bz2,fa.bz2,fas.bz2" label="Forward/single end (R1) Fasta file" />
        </when>
        <when value="pairedFasta">
          <param name="inputR1" type="data" format="fasta,fa,fas,fasta.gz,fa.gz,fas.gz,fasta.bz2,fa.bz2,fas.bz2" label="Forward/single end (R1) Fasta file" />
          <param name="inputR2" type="data" format="fasta,fa,fas,fasta.gz,fa.gz,fas.gz,fasta.bz2,fa.bz2,fas.bz2" label="Reverse (R2) Fasta file" />
        </when>
      </conditional>
    </inputs>
    <outputs>
      <data format="tabular" name="combineSummary" label="${tool.name} kt combine summary" />
      <data format="inputR1" name="outputAR1" label="${tool.name} (class A) filtered R1-reads of ${on_string}" />
      <data format="inputR2" name="outputAR2" label="${tool.name} (class A) filtered R2-reads of ${on_string}">
        <filter>inputFormat == "pairedFastq" or inputFormat == "pairedFasta</filter>
      </data>
    <data format="inputR1" name="outputBR1" label="${tool.name} (class B) filtered R1-reads of ${on_string}" />
    <data format="inputR2" name="outputBR2" label="${tool.name} (class B) filtered R2-reads of ${on_string}">
      <filter>inputFormat == "pairedFastq" or inputFormat == "pairedFasta</filter>
    </data>
    <data format="inputR1" name="outputABR1" label="${tool.name} (class AB) filtered R1-reads of ${on_string}" />
    <data format="inputR2" name="outputABR2" label="${tool.name} (class AB) filtered R2-reads of ${on_string}">
      <filter>inputFormat == "pairedFastq" or inputFormat == "pairedFasta</filter>
    </data>
    <data format="inputR1" name="outputUR1" label="${tool.name} (unclassified) filtered R1-reads of ${on_string}" />
    <data format="inputR2" name="outputUR2" label="${tool.name} (unclassified) filtered R2-reads of ${on_string}">
      <filter>inputFormat == "pairedFastq" or inputFormat == "pairedFasta</filter>
    </data>
  </outputs>
    <help><![CDATA[
        TODO: Fill in help.
    ]]></help>
</tool>