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comparison stacks_clonefilter.xml @ 0:1b6d07160736 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
author iuc
date Mon, 01 Jul 2019 10:57:08 -0400
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children b75174403a65
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-1:000000000000 0:1b6d07160736
1 <tool id="stacks2_clonefilter" name="Stacks2: clone filter" profile="@PROFILE@" version="@STACKS_VERSION@+galaxy@WRAPPER_VERSION@">
2 <description>Identify PCR clones</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <expand macro="version_cmd"/>
8 <command detect_errors="aggressive"><![CDATA[
9 @FASTQ_INPUT_FUNCTIONS@
10
11 mkdir stacks_inputs stacks_outputs &&
12
13 #set ($link_command, $fwd_path, $rev_path, $inputype) = $fastq_input_batch($input_type.fqinputs, $input_type.input_type_select)
14 $link_command
15
16 clone_filter
17 #if $input_type.input_type_select == 'single':
18 -f '$fwd_path'
19 #else
20 -1 '$fwd_path'
21 -2 '$rev_path'
22 #end if
23
24 -i $inputype
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
39 @TEE_APPEND_LOG@
40 @CAT_LOG_TO_STDERR@
41
42 ## move outputs such that Galaxy can find them
43 #if $capture:
44 #if $input_type.input_type_select == "single"
45 && mv stacks_outputs/*.discards.fq.gz '$discarded'
46 #else
47 && mv stacks_outputs/*.discards.1.fq.gz '$discarded_pair.forward'
48 && mv stacks_outputs/*.discards.2.fq.gz '$discarded_pair.reverse'
49 #end if
50 #end if
51 #if $input_type.input_type_select == "single"
52 && mv stacks_outputs/*.fq.gz '$clean'
53 #else
54 && mv stacks_outputs/*.1.fq.gz '$clean_pair.forward'
55 && mv stacks_outputs/*.2.fq.gz '$clean_pair.reverse'
56 #end if
57 ]]></command>
58 <inputs>
59 <expand macro="fastq_input_bc"/>
60 <param name="capture" type="boolean" checked="false" truevalue="-D" falsevalue="" argument="-D" label="Capture discarded reads to a file" />
61 <param name="oligo_len_1" type="integer" value="0" label="Length of the single-end oligo sequence in dataset"/>
62 <param name="oligo_len_2" optional="true" type="integer" label="Length of the paired-end oligo sequence in dataset"/>
63 <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)" />
64 <expand macro="in_log"/>
65 </inputs>
66 <outputs>
67 <expand macro="out_log"/>
68 <data format="fastqsanger.gz" name="clean" from_work_dir="outputs/R1.fq.gz" label="${tool.name} on ${on_string}">
69 <filter>input_type['input_type_select'] == 'single'</filter>
70 </data>
71 <collection name="clean_pair" type="paired" label="${tool.name} on ${on_string}">
72 <filter>input_type['input_type_select'] == 'paired'</filter>
73 </collection>
74 <data name="discarded" format="fastqsanger" label="${tool.name} on ${on_string}: discarded reads">
75 <filter>capture and input_type['input_type_select'] == 'single' and not options_kmer_char['k_dist']</filter>
76 </data>
77 <collection name="discarded_pair" type="paired" label="${tool.name} on ${on_string}: discarded reads">
78 <filter>capture and input_type['input_type_select'] == 'paired' and not options_kmer_char['k_dist']</filter>
79 </collection>
80 </outputs>
81 <tests>
82 <!-- single end, defaults-->
83 <test>
84 <conditional name="input_type">
85 <param name="input_type_select" value="single" />
86 <param name="fqinputs" ftype="fastqsanger.gz" value="clonefilter/R1_0001.1.fq.gz" />
87 </conditional>
88 <param name="oligo_len_1" value="6" />
89 <param name="add_log" value="yes" />
90 <output name="output_log" ftype="txt" file="clonefilter/clonefilter.log" lines_diff="8"/>
91 <output name="clean" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.single.gz"/>
92 </test>
93 <!-- single end, alt BCencoding, capture-->
94 <test>
95 <conditional name="input_type">
96 <param name="input_type_select" value="single" />
97 <param name="fqinputs" ftype="fastqsanger.gz" value="clonefilter/R1_0001.1.fq.gz" />
98 <param name="barcode_encoding" value="--index_null" />
99 </conditional>
100 <param name="capture" value="-D" />
101 <param name="oligo_len_1" value="6" />
102 <assert_command>
103 <has_text text="-D" />
104 </assert_command>
105 <output name="clean" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.gz"/>
106 <output name="discarded" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.gz"/>
107 </test>
108 <!-- paired end, defaults-->
109 <test>
110 <conditional name="input_type">
111 <param name="input_type_select" value="paired" />
112 <param name="fqinputs">
113 <collection type="paired">
114 <element name="forward" value="clonefilter/R1_0001.1.fq.gz" />
115 <element name="reverse" value="clonefilter/R2_0001.2.fq.gz" />
116 </collection>
117 </param>
118 </conditional>
119 <param name="oligo_len_1" value="6" />
120 <output_collection name="clean_pair" type="paired">
121 <element name="forward" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.gz" />
122 <element name="reverse" compare="sim_size" file="clonefilter/Removed2_0001.2.2.fq.gz" />
123 </output_collection>
124 </test>
125 <!-- paired end, non defaults -->
126 <test>
127 <conditional name="input_type">
128 <param name="input_type_select" value="paired" />
129 <param name="fqinputs">
130 <collection type="paired">
131 <element name="forward" value="clonefilter/R1_0001.1.fq.gz" />
132 <element name="reverse" value="clonefilter/R2_0001.2.fq.gz" />
133 </collection>
134 </param>
135 </conditional>
136 <param name="oligo_len_1" value="6" />
137 <param name="capture" value="-D" />
138 <param name="retain_oligo" value="--retain_oligo" />
139 <assert_command>
140 <has_text text="--retain_oligo" />
141 </assert_command>
142 <output_collection name="clean_pair" type="paired">
143 <element name="forward" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.gz" />
144 <element name="reverse" compare="sim_size" file="clonefilter/Removed2_0001.2.2.fq.gz" />
145 </output_collection>
146 <output_collection name="discarded_pair" type="paired">
147 <element name="forward" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.gz" />
148 <element name="reverse" compare="sim_size" file="clonefilter/Removed2_0001.2.2.fq.gz" />
149 </output_collection>
150 </test>
151 </tests>
152 <help>
153 <![CDATA[
154 .. class:: infomark
155
156 The clone_filter program is designed to identify PCR clones.
157
158 @STACKS_INFOS@
159 ]]>
160 </help>
161 <expand macro="citation" />
162 </tool>