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comparison stacks_clonefilter.xml @ 5:c4ed7dacee9b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 4e87a14a5479800df9675c1cbcdbe1b11f63653b-dirty
author matthias
date Wed, 27 Feb 2019 10:03:16 -0500
parents 4758a347d62e
children b707e9def9ff
comparison
equal deleted inserted replaced
4:d98470ab842e 5:c4ed7dacee9b
1 <tool id="stacks2_clonefilter" name="Stacks2: clone filter" version="@STACKS_VERSION@+galaxy@WRAPPER_VERSION@"> 1 <tool id="stacks2_clonefilter" name="Stacks2: clone filter" profile="@PROFILE@" version="@STACKS_VERSION@+galaxy@WRAPPER_VERSION@">
2 <description>Identify PCR clones</description> 2 <description>Identify PCR clones</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="stdio"/>
8 <expand macro="version_cmd"/> 7 <expand macro="version_cmd"/>
9 <command><![CDATA[ 8 <command detect_errors="aggressive"><![CDATA[
10 #if $data_type.dt_select == "single" 9 @FASTQ_INPUT_FUNCTIONS@
11 10
12 #if $data_type.fname.is_of_type('fastqsanger') 11 mkdir stacks_inputs stacks_outputs &&
13 #set $ext = ".fq"
14 #set inputype = "fastq"
15 #else
16 #set $ext = ".fq.gz"
17 #set inputype = "gzfastq"
18 #end if
19 12
20 ln -s '$data_type.fname' R1$ext && 13 #set ($link_command, $fwd_path, $rev_path, $inputype) = $fastq_input_batch($input_type.fqinputs, $input_type.input_type_select)
21 #else 14 $link_command
22 15
23 #if $data_type.fwd.is_of_type('fastqsanger') 16 clone_filter
24 #set $ext = ".fq" 17 #if $input_type.input_type_select == 'single':
25 #set inputype = "fastq" 18 -f '$fwd_path'
26 #else 19 #else
27 #set $ext = ".fq.gz" 20 -1 '$fwd_path'
28 #set inputype = "gzfastq" 21 -2 '$rev_path'
29 #end if 22 #end if
30 23
31 ln -s '$data_type.fwd' R1$ext && 24 -i $inputype
32 ln -s '$data_type.rev' R2$ext &&
33 #end if
34 25
26 -o stacks_outputs
27 $capture
28 $input_type.barcode_encoding
29 #if $oligo_len_1
30 --oligo_len_1 $oligo_len_1
31 #end if
32 #if $oligo_len_2
33 --oligo_len_2 $oligo_len_2
34 #end if
35 $retain_oligo
36 ## only supports fastq.gz output since the
37 ## the program outputs empty files for fasta/fastq
38 -y gzfastq
35 39
36 mkdir outputs 40 ## move outputs such that Galaxy can find them
37 41 #if $capture:
38 && 42 #if $input_type.input_type_select == "single"
39 43 && mv stacks_outputs/*.discards.fq.gz '$discarded'
40 clone_filter 44 #else
41 #if $data_type.dt_select == 'single': 45 && mv stacks_outputs/*.discards.1.fq.gz '$discarded_pair.forward'
42 -f R1$ext 46 && mv stacks_outputs/*.discards.2.fq.gz '$discarded_pair.reverse'
43 #else 47 #end if
44 -1 R1$ext 48 #end if
45 -2 R2$ext 49 #if $input_type.input_type_select == "single"
46 #end if 50 && mv stacks_outputs/*.fq.gz '$clean'
47 51 #else
48 -i $inputype 52 && mv stacks_outputs/*.1.fq.gz '$clean_pair.forward'
49 53 && mv stacks_outputs/*.2.fq.gz '$clean_pair.reverse'
50 -o outputs 54 #end if
51 $capture 55 ]]></command>
52 $data_type.barcode_encoding
53 #if $oligo_len_1
54 --oligo_len_1 $oligo_len_1
55 #end if
56 #if $oligo_len_2
57 --oligo_len_2 $oligo_len_2
58 #end if
59 $retain_oligo
60 ## only supports fastq.gz output since the
61 ## the program outputs empty files for fasta/fastq
62 -y gzfastq
63 ]]></command>
64 <inputs> 56 <inputs>
65 <conditional name="data_type"> 57 <expand macro="fastq_input_bc"/>
66 <param name="dt_select" type="select" label="Single or Paired-end">
67 <option value="single">Single</option>
68 <option value="pair">Pair</option>
69 </param>
70 <when value="single">
71 <param name="fname" type="data" format="fastqsanger,fastqsanger.gz" label="FASTQ" />
72 <param name="barcode_encoding" type="select" label="Barcode location">
73 <expand macro="barcode_encoding_single" type="Random oligo"/>
74 </param>
75
76 </when>
77 <when value="pair">
78 <param name="fwd" type="data" format="fastqsanger,fastqsanger.gz" label="Forward FASTQ" />
79 <param name="rev" type="data" format="fastqsanger,fastqsanger.gz" label="Reverse FASTQ" />
80 <param name="barcode_encoding" type="select" label="Barcode location">
81 <expand macro="barcode_encoding_pair" type="Random oligo"/>
82 </param>
83 </when>
84 </conditional>
85 <param name="capture" type="boolean" checked="false" truevalue="-D" falsevalue="" argument="-D" label="Capture discarded reads to a file" /> 58 <param name="capture" type="boolean" checked="false" truevalue="-D" falsevalue="" argument="-D" label="Capture discarded reads to a file" />
86 <param name="oligo_len_1" type="integer" value="0" label="length of the single-end oligo sequence in data set"/> 59 <param name="oligo_len_1" type="integer" value="0" label="Length of the single-end oligo sequence in dataset"/>
87 <param name="oligo_len_2" optional="true" type="integer" label="length of the paired-end oligo sequence in data set"/> 60 <param name="oligo_len_2" optional="true" type="integer" label="Length of the paired-end oligo sequence in dataset"/>
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)" /> 61 <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)" />
89
90 </inputs> 62 </inputs>
91 <outputs> 63 <outputs>
92 <data format="fastqsanger.gz" name="clean" from_work_dir="outputs/R1.fq.gz" label="${tool.name} on ${on_string}"> 64 <data format="fastqsanger.gz" name="clean" from_work_dir="outputs/R1.fq.gz" label="${tool.name} on ${on_string}">
93 <filter>data_type['dt_select'] == 'single'</filter> 65 <filter>input_type['input_type_select'] == 'single'</filter>
94 </data> 66 </data>
95 67 <collection name="clean_pair" type="paired" label="${tool.name} on ${on_string}">
96 <data format="fastqsanger.gz" name="clean_fwd" from_work_dir="outputs/R1.1.fq.gz" label="${tool.name} on ${on_string} Forward reads"> 68 <filter>input_type['input_type_select'] == 'paired'</filter>
97 <filter>data_type['dt_select'] == 'pair'</filter> 69 </collection>
70 <data name="discarded" format="fastqsanger" label="${tool.name} on ${on_string}: discarded reads">
71 <filter>capture and input_type['input_type_select'] == 'single' and not options_kmer_char['k_dist']</filter>
98 </data> 72 </data>
99 <data format="fastqsanger.gz" name="clean_rev" from_work_dir="outputs/R2.2.fq.gz" label="${tool.name} on ${on_string} Reverse reads"> 73 <collection name="discarded_pair" type="paired" label="${tool.name} on ${on_string}: discarded reads">
100 <filter>data_type['dt_select'] == 'pair'</filter> 74 <filter>capture and input_type['input_type_select'] == 'paired' and not options_kmer_char['k_dist']</filter>
101 </data> 75 </collection>
102 </outputs> 76 </outputs>
103 <tests> 77 <tests>
104 <!-- single end, defaults--> 78 <!-- single end, defaults-->
105 <test> 79 <test>
106 <conditional name="data_type"> 80 <conditional name="input_type">
107 <param name="dt_select" value="single" /> 81 <param name="input_type_select" value="single" />
108 <param name="fname" ftype="fastqsanger.gz" value="clonefilter/R1_0001.1.fq.gz" /> 82 <param name="fqinputs" ftype="fastqsanger.gz" value="clonefilter/R1_0001.1.fq.gz" />
109 </conditional> 83 </conditional>
110 <param name="oligo_len_1" value="6" /> 84 <param name="oligo_len_1" value="6" />
111 <output name="clean" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.single.gz"/> 85 <output name="clean" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.single.gz"/>
112 </test> 86 </test>
113 <!-- single end, alt BCencoding, capture--> 87 <!-- single end, alt BCencoding, capture-->
114 <test> 88 <test>
115 <conditional name="data_type"> 89 <conditional name="input_type">
116 <param name="dt_select" value="single" /> 90 <param name="input_type_select" value="single" />
117 <param name="fname" ftype="fastqsanger.gz" value="clonefilter/R1_0001.1.fq.gz" /> 91 <param name="fqinputs" ftype="fastqsanger.gz" value="clonefilter/R1_0001.1.fq.gz" />
118 <param name="barcode_encoding" value="--index_null" /> 92 <param name="barcode_encoding" value="--index_null" />
119 </conditional> 93 </conditional>
120 <param name="capture" value="-D" /> 94 <param name="capture" value="-D" />
121 <param name="oligo_len_1" value="6" /> 95 <param name="oligo_len_1" value="6" />
122 <assert_command> 96 <assert_command>
123 <has_text text="-D" /> 97 <has_text text="-D" />
124 </assert_command> 98 </assert_command>
125 <output name="clean" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.gz"/> 99 <output name="clean" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.gz"/>
100 <output name="discarded" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.gz"/>
126 </test> 101 </test>
127 <!-- paired end, defaults--> 102 <!-- paired end, defaults-->
128 <test> 103 <test>
129 <conditional name="data_type"> 104 <conditional name="input_type">
130 <param name="dt_select" value="pair" /> 105 <param name="input_type_select" value="paired" />
131 <param name="fwd" ftype="fastqsanger" value="clonefilter/R1_0001.1.fq.gz" /> 106 <param name="fqinputs">
132 <param name="rev" ftype="fastqsanger" value="clonefilter/R2_0001.2.fq.gz" /> 107 <collection type="paired">
108 <element name="forward" value="clonefilter/R1_0001.1.fq.gz" />
109 <element name="reverse" value="clonefilter/R2_0001.2.fq.gz" />
110 </collection>
111 </param>
133 </conditional> 112 </conditional>
134 <param name="oligo_len_1" value="6" /> 113 <param name="oligo_len_1" value="6" />
135 <output name="clean_fwd" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.gz"/> 114 <output_collection name="clean_pair" type="paired">
136 <output name="clean_rev" compare="sim_size" file="clonefilter/Removed2_0001.2.2.fq.gz"/> 115 <element name="forward" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.gz" />
116 <element name="reverse" compare="sim_size" file="clonefilter/Removed2_0001.2.2.fq.gz" />
117 </output_collection>
137 </test> 118 </test>
138 <!-- paired end, non defaults--> 119 <!-- paired end, non defaults -->
139 <test> 120 <test>
140 <conditional name="data_type"> 121 <conditional name="input_type">
141 <param name="dt_select" value="pair" /> 122 <param name="input_type_select" value="paired" />
142 <param name="fwd" ftype="fastqsanger.gz" value="clonefilter/R1_0001.1.fq.gz" /> 123 <param name="fqinputs">
143 <param name="rev" ftype="fastqsanger.gz" value="clonefilter/R2_0001.2.fq.gz" /> 124 <collection type="paired">
125 <element name="forward" value="clonefilter/R1_0001.1.fq.gz" />
126 <element name="reverse" value="clonefilter/R2_0001.2.fq.gz" />
127 </collection>
128 </param>
144 </conditional> 129 </conditional>
145 <param name="oligo_len_1" value="6" /> 130 <param name="oligo_len_1" value="6" />
146 <param name="capture" value="-D" /> 131 <param name="capture" value="-D" />
147 <param name="retain_oligo" value="--retain_oligo" /> 132 <param name="retain_oligo" value="--retain_oligo" />
148 <assert_command> 133 <assert_command>
149 <has_text text="--retain_oligo" /> 134 <has_text text="--retain_oligo" />
150 </assert_command> 135 </assert_command>
151 <output name="clean_fwd" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.gz"/> 136 <output_collection name="clean_pair" type="paired">
152 <output name="clean_rev" compare="sim_size" file="clonefilter/Removed2_0001.2.2.fq.gz"/> 137 <element name="forward" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.gz" />
138 <element name="reverse" compare="sim_size" file="clonefilter/Removed2_0001.2.2.fq.gz" />
139 </output_collection>
140 <output_collection name="discarded_pair" type="paired">
141 <element name="forward" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.gz" />
142 <element name="reverse" compare="sim_size" file="clonefilter/Removed2_0001.2.2.fq.gz" />
143 </output_collection>
153 </test> 144 </test>
154 </tests> 145 </tests>
155 <help> 146 <help>
156 <![CDATA[ 147 <![CDATA[
157 .. class:: infomark 148 .. class:: infomark