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comparison micall_lite.xml @ 0:023064145bea draft

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"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
author public-health-bioinformatics
date Mon, 06 Jan 2020 19:10:15 -0500
parents
children bb549c5eaf34
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-1:000000000000 0:023064145bea
1 <tool id="micall_lite" name="micall_lite" version="@TOOL_VERSION@+galaxy0">
2 <description></description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <requirements>
7 <requirement type="package" version="@TOOL_VERSION@">micall-lite</requirement>
8 </requirements>
9 <version_command>echo "@TOOL_VERSION@"</version_command>
10 <command detect_errors="exit_code">
11 <![CDATA[
12 #if str( $fastq_input.fastq_input_selector ) == "paired":
13 #if $fastq_input.reads1.is_of_type("fastq.gz", "fastqsanger.gz"):
14 #set unzipped = False
15 #set reads1 = $fastq_input.reads1.element_identifier + '_R1.fastq.gz'
16 #else if $fastq_input.reads1.is_of_type("fastq", "fastqsanger"):
17 #set unzipped = True
18 #set reads1 = $fastq_input.reads1.element_identifier + '_R1.fastq'
19 #end if
20 ln -s '$fastq_input.reads1' '$reads1' &&
21 #if $fastq_input.reads2.is_of_type("fastq.gz", "fastqsanger.gz"):
22 #set unzipped = False
23 #set reads2 = $fastq_input.reads2.element_identifier + '_R2.fastq.gz'
24 #else if $fastq_input.reads2.is_of_type("fastq", "fastqsanger"):
25 #set unzipped = True
26 #set reads2 = $fastq_input.reads2.element_identifier + '_R2.fastq'
27 #end if
28 ln -s '$fastq_input.reads2' '$reads2' &&
29 #else if str( $fastq_input.fastq_input_selector ) == "paired_collection":
30 #if $fastq_input.pair.forward.is_of_type("fastq.gz", "fastqsanger.gz"):
31 #set unzipped = False
32 #set reads1 = $fastq_input.pair.element_identifier + '_R1.fastq.gz'
33 #else if $fastq_input.pair.forward.is_of_type("fastq", "fastqsanger"):
34 #set unzipped = True
35 #set reads1 = $fastq_input.pair.element_identifier + '_R1.fastq'
36 #end if
37 ln -s '$fastq_input.pair.forward' '$reads1' &&
38 #if $fastq_input.pair.reverse.is_of_type("fastq.gz", "fastqsanger.gz"):
39 #set unzipped = False
40 #set reads2 = $fastq_input.pair.element_identifier + '_R2.fastq.gz'
41 #else if $fastq_input.pair.reverse.is_of_type("fastq", "fastqsanger"):
42 #set unzipped = True
43 #set reads2 = $fastq_input.pair.element_identifier + '_R2.fastq'
44 #end if
45 ln -s '$fastq_input.pair.reverse' '$reads2' &&
46 #end if
47
48 mkdir 'outdir' &&
49 micall
50 --threads \${GALAXY_SLOTS:-1}
51 #if $unzipped:
52 --unzipped
53 #end if
54 --readlen ${readlen}
55 '${reads1}'
56 '${reads2}'
57 --outdir 'outdir'
58 ]]>
59 </command>
60 <inputs>
61 <conditional name="fastq_input">
62 <param name="fastq_input_selector" type="select" label="Paired Reads or Paired Collection" >
63 <option selected="true" value="paired">Paired</option>
64 <option value="paired_collection">Paired Collection</option>
65 </param>
66 <when value="paired">
67 <param format="@INTYPES@" name="reads1" type="data" label="Select first set of reads"/>
68 <param format="@INTYPES@" name="reads2" type="data" label="Select second set of reads"/>
69 </when>
70 <when value="paired_collection">
71 <param format="@INTYPES@" name="pair" type="data_collection" collection_type="paired" label="Collection of paired reads"/>
72 </when>
73 </conditional>
74 <param name="readlen" type="integer" min="1" value="251" max="600" label="Read Length" help="Read Length" />
75 </inputs>
76 <outputs>
77 <data name="align" label="align" format="csv" from_work_dir="outdir/*.align.csv" />
78 <data name="amino" label="amino" format="csv" from_work_dir="outdir/*.amino.csv" />
79 <data name="conseq" label="conseq" format="csv" from_work_dir="outdir/*.conseq.csv" />
80 <data name="insert" label="insert" format="csv" from_work_dir="outdir/*.insert.csv" />
81 <data name="nuc" label="nuc" format="csv" from_work_dir="outdir/*.nuc.csv" />
82 </outputs>
83 <tests>
84 <test>
85 <conditional name="fastq_input">
86 <param name="fastq_input_selector" value="paired"/>
87 <param name="reads1" value="1234A-V3LOOP_S1_L001_R1_001.fastq" />
88 <param name="reads2" value="1234A-V3LOOP_S1_L001_R2_001.fastq" />
89 </conditional>
90 <param name="readlen" value="51" />
91 <output name="align" value="1234A-V3LOOP.align.csv" />
92 <output name="amino" value="1234A-V3LOOP.amino.csv" />
93 <output name="conseq" value="1234A-V3LOOP.conseq.csv" />
94 <output name="insert" value="1234A-V3LOOP.insert.csv" />
95 <output name="nuc" value="1234A-V3LOOP.nuc.csv" />
96 </test>
97 <test>
98 <conditional name="fastq_input">
99 <param name="fastq_input_selector" value="paired"/>
100 <param name="reads1" value="1234A-V3LOOP_S1_L001_R1_001.fastq.gz" />
101 <param name="reads2" value="1234A-V3LOOP_S1_L001_R2_001.fastq.gz" />
102 </conditional>
103 <param name="readlen" value="51" />
104 <output name="align" value="1234A-V3LOOP.align.csv" />
105 <output name="amino" value="1234A-V3LOOP.amino.csv" />
106 <output name="conseq" value="1234A-V3LOOP.conseq.csv" />
107 <output name="insert" value="1234A-V3LOOP.insert.csv" />
108 <output name="nuc" value="1234A-V3LOOP.nuc.csv" />
109 </test>
110 <test>
111 <conditional name="fastq_input">
112 <param name="fastq_input_selector" value="paired_collection" />
113 <param name="pair" >
114 <collection type="paired">
115 <element name="forward" value="1234A-V3LOOP_S1_L001_R1_001.fastq" />
116 <element name="reverse" value="1234A-V3LOOP_S1_L001_R2_001.fastq" />
117 </collection>
118 </param>
119 </conditional>
120 <param name="readlen" value="51" />
121 <output name="align" value="1234A-V3LOOP.align.csv" />
122 <output name="amino" value="1234A-V3LOOP.amino.csv" />
123 <output name="conseq" value="1234A-V3LOOP.conseq.csv" />
124 <output name="insert" value="1234A-V3LOOP.insert.csv" />
125 <output name="nuc" value="1234A-V3LOOP.nuc.csv" />
126 </test>
127 <test>
128 <conditional name="fastq_input">
129 <param name="fastq_input_selector" value="paired_collection" />
130 <param name="pair" >
131 <collection type="paired">
132 <element name="forward" value="1234A-V3LOOP_S1_L001_R1_001.fastq.gz" />
133 <element name="reverse" value="1234A-V3LOOP_S1_L001_R2_001.fastq.gz" />
134 </collection>
135 </param>
136 </conditional>
137 <param name="readlen" value="51" />
138 <output name="align" value="1234A-V3LOOP.align.csv" />
139 <output name="amino" value="1234A-V3LOOP.amino.csv" />
140 <output name="conseq" value="1234A-V3LOOP.conseq.csv" />
141 <output name="insert" value="1234A-V3LOOP.insert.csv" />
142 <output name="nuc" value="1234A-V3LOOP.nuc.csv" />
143 </test>
144 </tests>
145 <help><![CDATA[
146 ]]></help>
147 <expand macro="citations" />
148 </tool>