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comparison stacks_clonefilter.xml @ 3:4758a347d62e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
author matthias
date Tue, 18 Dec 2018 13:06:09 -0500
parents 223e7778451a
children c4ed7dacee9b
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2:223e7778451a 3:4758a347d62e
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="stdio"/> 7 <expand macro="stdio"/>
8 <expand macro="version_cmd"/> 8 <expand macro="version_cmd"/>
9 <command><![CDATA[ 9 <command><![CDATA[
10
11 #if $data_type.dt_select == "single" 10 #if $data_type.dt_select == "single"
12 11
13 #if $data_type.fname.is_of_type('fastqsanger') 12 #if $data_type.fname.is_of_type('fastqsanger')
14 #set $ext = ".fq" 13 #set $ext = ".fq"
15 #set inputype = "fastq" 14 #set inputype = "fastq"
32 ln -s '$data_type.fwd' R1$ext && 31 ln -s '$data_type.fwd' R1$ext &&
33 ln -s '$data_type.rev' R2$ext && 32 ln -s '$data_type.rev' R2$ext &&
34 #end if 33 #end if
35 34
36 35
37 mkdir clone_outputs 36 mkdir outputs
38 37
39 && 38 &&
40 39
41 clone_filter 40 clone_filter
42 #if $data_type.dt_select == 'single': 41 #if $data_type.dt_select == 'single':
46 -2 R2$ext 45 -2 R2$ext
47 #end if 46 #end if
48 47
49 -i $inputype 48 -i $inputype
50 49
51 -o clone_outputs 50 -o outputs
52 $capture 51 $capture
53 52 $data_type.barcode_encoding
54 #if $oligo_len_1 53 #if $oligo_len_1
55 --oligo_len_1 $oligo_len_1 54 --oligo_len_1 $oligo_len_1
56 $data_type.barcode_encoding
57 #end if 55 #end if
58 #if $oligo_len_2 56 #if $oligo_len_2
59 --oligo_len_2 $oligo_len_2 57 --oligo_len_2 $oligo_len_2
60 #end if 58 #end if
61 $retain_oligo 59 $retain_oligo
62 ## only supports fastq.gz output since the 60 ## only supports fastq.gz output since the
63 ## the program outputs empty files for fasta/fastq 61 ## the program outputs empty files for fasta/fastq
64 -y gzfastq 62 -y gzfastq
65
66 ]]></command> 63 ]]></command>
67 <inputs> 64 <inputs>
68 <conditional name="data_type"> 65 <conditional name="data_type">
69 <param name="dt_select" type="select" label="Single or Paired-end"> 66 <param name="dt_select" type="select" label="Single or Paired-end">
70 <option value="single">Single</option> 67 <option value="single">Single</option>
71 <option value="pair">Pair</option> 68 <option value="pair">Pair</option>
72 </param> 69 </param>
73 <when value="single"> 70 <when value="single">
74 <param name="fname" type="data" format="fastqsanger,fastqsanger.gz" label="FASTQ" /> 71 <param name="fname" type="data" format="fastqsanger,fastqsanger.gz" label="FASTQ" />
75 <param name="barcode_encoding" type="select" label="Barcode location"> 72 <param name="barcode_encoding" type="select" label="Barcode location">
76 <expand macro="barcode_encoding_single" /> 73 <expand macro="barcode_encoding_single" type="Random oligo"/>
77 </param> 74 </param>
78 75
79 </when> 76 </when>
80 <when value="pair"> 77 <when value="pair">
81 <param name="fwd" type="data" format="fastqsanger,fastqsanger.gz" label="Forward FASTQ" /> 78 <param name="fwd" type="data" format="fastqsanger,fastqsanger.gz" label="Forward FASTQ" />
82 <param name="rev" type="data" format="fastqsanger,fastqsanger.gz" label="Reverse FASTQ" /> 79 <param name="rev" type="data" format="fastqsanger,fastqsanger.gz" label="Reverse FASTQ" />
83 <param name="barcode_encoding" type="select" label="Barcode location"> 80 <param name="barcode_encoding" type="select" label="Barcode location">
84 <expand macro="barcode_encoding_pair" /> 81 <expand macro="barcode_encoding_pair" type="Random oligo"/>
85 </param> 82 </param>
86 </when> 83 </when>
87 </conditional> 84 </conditional>
88 <param name="capture" type="boolean" checked="false" truevalue="-D" falsevalue="" argument="-D" label="Capture discarded reads to a file" /> 85 <param name="capture" type="boolean" checked="false" truevalue="-D" falsevalue="" argument="-D" label="Capture discarded reads to a file" />
89 <param name="oligo_len_1" optional="true" type="integer" label="length of the single-end oligo sequence in data set"/> 86 <param name="oligo_len_1" type="integer" value="0" label="length of the single-end oligo sequence in data set"/>
90 <param name="oligo_len_2" optional="true" type="integer" label="length of the paired-end oligo sequence in data set"/> 87 <param name="oligo_len_2" optional="true" type="integer" label="length of the paired-end oligo sequence in data set"/>
91 <param argument="--retain_oligo" type="boolean" checked="false" truevalue="--retain_oligo" falsevalue="" label="do not trim off the random oligo sequence (if oligo is inline)" /> 88 <param argument="--retain_oligo" type="boolean" checked="false" truevalue="--retain_oligo" falsevalue="" label="do not trim off the random oligo sequence (if oligo is inline)" />
92 89
93 </inputs> 90 </inputs>
94 <outputs> 91 <outputs>
95 <data format="fastqsanger.gz" name="clean" from_work_dir="clone_outputs/R1.fq.gz" label="${tool.name} on ${on_string}"> 92 <data format="fastqsanger.gz" name="clean" from_work_dir="outputs/R1.fq.gz" label="${tool.name} on ${on_string}">
96 <filter>data_type['dt_select'] == 'single'</filter> 93 <filter>data_type['dt_select'] == 'single'</filter>
97 </data> 94 </data>
98 95
99 <data format="fastqsanger.gz" name="clean_fwd" from_work_dir="clone_outputs/R1.1.fq.gz" label="${tool.name} on ${on_string} Forward reads"> 96 <data format="fastqsanger.gz" name="clean_fwd" from_work_dir="outputs/R1.1.fq.gz" label="${tool.name} on ${on_string} Forward reads">
100 <filter>data_type['dt_select'] == 'pair'</filter> 97 <filter>data_type['dt_select'] == 'pair'</filter>
101 </data> 98 </data>
102 <data format="fastqsanger.gz" name="clean_rev" from_work_dir="clone_outputs/R2.2.fq.gz" label="${tool.name} on ${on_string} Reverse reads"> 99 <data format="fastqsanger.gz" name="clean_rev" from_work_dir="outputs/R2.2.fq.gz" label="${tool.name} on ${on_string} Reverse reads">
103 <filter>data_type['dt_select'] == 'pair'</filter> 100 <filter>data_type['dt_select'] == 'pair'</filter>
104 </data> 101 </data>
105 </outputs> 102 </outputs>
106 <tests> 103 <tests>
104 <!-- single end, defaults-->
107 <test> 105 <test>
108 <conditional name="data_type"> 106 <conditional name="data_type">
109 <param name="dt_select" value="single" /> 107 <param name="dt_select" value="single" />
110 <param name="fname" ftype="fastqsanger.gz" value="clonefilter/R1_0001.1.fq.gz" /> 108 <param name="fname" ftype="fastqsanger.gz" value="clonefilter/R1_0001.1.fq.gz" />
111 </conditional> 109 </conditional>
112 <param name="oligo_len_1" value="6" /> 110 <param name="oligo_len_1" value="6" />
113 <output name="clean" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.single.gz"/> 111 <output name="clean" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.single.gz"/>
114 </test> 112 </test>
113 <!-- single end, alt BCencoding, capture-->
115 <test> 114 <test>
116 <conditional name="data_type"> 115 <conditional name="data_type">
117 <param name="dt_select" value="single" /> 116 <param name="dt_select" value="single" />
118 <param name="fname" ftype="fastqsanger.gz" value="clonefilter/R1_0001.1.fq.gz" /> 117 <param name="fname" ftype="fastqsanger.gz" value="clonefilter/R1_0001.1.fq.gz" />
119 <param name="barcode_encoding" value="--index_null" /> 118 <param name="barcode_encoding" value="--index_null" />
120 </conditional> 119 </conditional>
120 <param name="capture" value="-D" />
121 <param name="oligo_len_1" value="6" />
122 <assert_command>
123 <has_text text="-D" />
124 </assert_command>
121 <output name="clean" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.gz"/> 125 <output name="clean" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.gz"/>
122 </test> 126 </test>
127 <!-- paired end, defaults-->
123 <test> 128 <test>
124 <conditional name="data_type"> 129 <conditional name="data_type">
125 <param name="dt_select" value="pair" /> 130 <param name="dt_select" value="pair" />
126 <param name="fwd" ftype="fastqsanger" value="clonefilter/R1_0001.1.fq.gz" /> 131 <param name="fwd" ftype="fastqsanger" value="clonefilter/R1_0001.1.fq.gz" />
127 <param name="rev" ftype="fastqsanger" value="clonefilter/R2_0001.2.fq.gz" /> 132 <param name="rev" ftype="fastqsanger" value="clonefilter/R2_0001.2.fq.gz" />
128 </conditional> 133 </conditional>
134 <param name="oligo_len_1" value="6" />
129 <output name="clean_fwd" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.gz"/> 135 <output name="clean_fwd" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.gz"/>
130 <output name="clean_rev" compare="sim_size" file="clonefilter/Removed2_0001.2.2.fq.gz"/> 136 <output name="clean_rev" compare="sim_size" file="clonefilter/Removed2_0001.2.2.fq.gz"/>
131 </test> 137 </test>
138 <!-- paired end, non defaults-->
132 <test> 139 <test>
133 <conditional name="data_type"> 140 <conditional name="data_type">
134 <param name="dt_select" value="pair" /> 141 <param name="dt_select" value="pair" />
135 <param name="fwd" ftype="fastqsanger.gz" value="clonefilter/R1_0001.1.fq.gz" /> 142 <param name="fwd" ftype="fastqsanger.gz" value="clonefilter/R1_0001.1.fq.gz" />
136 <param name="rev" ftype="fastqsanger.gz" value="clonefilter/R2_0001.2.fq.gz" /> 143 <param name="rev" ftype="fastqsanger.gz" value="clonefilter/R2_0001.2.fq.gz" />
137 </conditional> 144 </conditional>
145 <param name="oligo_len_1" value="6" />
146 <param name="capture" value="-D" />
147 <param name="retain_oligo" value="--retain_oligo" />
148 <assert_command>
149 <has_text text="--retain_oligo" />
150 </assert_command>
138 <output name="clean_fwd" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.gz"/> 151 <output name="clean_fwd" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.gz"/>
139 <output name="clean_rev" compare="sim_size" file="clonefilter/Removed2_0001.2.2.fq.gz"/> 152 <output name="clean_rev" compare="sim_size" file="clonefilter/Removed2_0001.2.2.fq.gz"/>
140 </test> 153 </test>
141 </tests> 154 </tests>
142 <help> 155 <help>
143 <![CDATA[ 156 <![CDATA[
144 .. class:: infomark 157 .. class:: infomark
145 158
146
147 The clone_filter program is designed to identify PCR clones. 159 The clone_filter program is designed to identify PCR clones.
148 160
149 @STACKS_INFOS@ 161 @STACKS_INFOS@
150 ]]> 162 ]]>
151 </help> 163 </help>