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comparison stacks_shortreads.xml @ 0:ad7a60726fc3 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 11:02:39 -0400
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-1:000000000000 0:ad7a60726fc3
1 <!-- this is essentially a copy of stacks_procrad minus the unsupported options -->
2 <tool id="stacks2_shortreads" name="Stacks2: process shortreads" profile="@PROFILE@" version="@STACKS_VERSION@+galaxy@WRAPPER_VERSION@">
3 <description>fast cleaning of randomly sheared genomic or transcriptomic data</description>
4 <macros>
5 <import>macros.xml</import>
6 <import>macros_process.xml</import>
7 </macros>
8 <expand macro="requirements"/>
9 <expand macro="version_cmd"/>
10 <command detect_errors="aggressive"><![CDATA[
11 @FASTQ_INPUT_FUNCTIONS@
12
13 mkdir stacks_inputs stacks_outputs &&
14
15 #set ($link_command, $inputype) = $fastq_input_nonbatch( $input_type.fqinputs, $input_type.input_type_select, "_R%d_0" )
16 $link_command
17
18
19 process_shortreads
20
21 @PROCESS_IOOPTIONS@
22 @PROCESS_FILTER@
23 @COMMON_ADVANCED@
24 @RESCUE_BARCODE@
25 @PROCESS_ADAPTER@
26
27 ## advanced options not shared between shortreads and radtags
28 $options_advanced.no_read_trimming
29 $options_advanced.mate_pair
30 $options_advanced.no_overhang
31
32 #if $output_log
33 && mv stacks_outputs/process_shortreads.log $output_log
34 #end if
35 @PROCESS_FASTQ_POSTPROC@
36 ]]></command>
37
38 <inputs>
39 <expand macro="fastq_input_bc_file" multiple="true" listtype="list:paired"/>
40 <section name="options_advanced" title="advanced options" expanded="False">
41 <expand macro="common_advanced"/>
42 <param argument="--no_read_trimming" type="boolean" checked="false" truevalue="--no_read_trimming" falsevalue="" label="Do not trim low quality reads, just discard them" />
43 <param argument="--mate-pair" name="mate_pair" type="boolean" checked="false" truevalue="--mate-pair" falsevalue="" label="Raw reads are circularized mate-pair data, first read will be reverse complemented" />
44 <param argument="--no_overhang" type="boolean" checked="false" truevalue="--no_overhang" falsevalue="" label="Data does not contain an overhang nucleotide between barcode and seqeunce" />
45 <expand macro="rescue_barcode"/>
46 <expand macro="process_adapter"/>
47 </section>
48 <expand macro="process_filter"/>
49 <expand macro="process_output_types"/>
50 </inputs>
51
52 <outputs>
53 <data format="txt" name="output_log" label="${tool.name} on ${on_string} log file" from_work_dir="stacks_outputs/process_shortreads.log" />
54 <expand macro="process_outputs"/>
55 </outputs>
56
57 <tests>
58 <!-- test single end, default options -->
59 <test>
60 <param name="input_type|input_type_select" value="single"/>
61 <param name="input_type|fqinputs" ftype="fastqsanger" value="procrad/R1.fq"/>
62 <param name="input_type|barcode_encoding" value="--inline_null"/>
63 <param name="barcode" value="procrad/barcodes"/>
64 <param name="add_log" value="yes" />
65 <output name="output_log" file="shortreads/process_shortreads.out" lines_diff="4"/>
66 <output_collection name="demultiplexed" count="40">
67 <element name="PopA_01" file="shortreads/PopA_01.fq" ftype="fastqsanger" />
68 </output_collection>
69 </test>
70 <!-- test single end, default options -->
71 <test>
72 <param name="input_type|input_type_select" value="paired"/>
73 <param name="input_type|fqinputs">
74 <collection type="list:paired">
75 <element name="reads">
76 <collection type="paired">
77 <element name="forward" value="procrad/R1.fq" ftype="fastqsanger" />
78 <element name="reverse" value="procrad/R2.fq" ftype="fastqsanger"/>
79 </collection>
80 </element>
81 </collection>
82 </param>
83 <param name="input_type|barcode_encoding" value="--inline_null"/>
84 <param name="barcode" value="procrad/barcodes"/>
85 <param name="capture" value="true"/>
86 <param name="no_read_trimming" value="--no_read_trimming" />
87 <param name="mate_pair" value="--mate-pair" />
88 <param name="no_overhang" value="--no_overhang" />
89 <param name="outype" value="gzfastq"/>
90 <param name="add_log" value="yes" />
91 <assert_command>
92 <has_text text="--no_read_trimming" />
93 <has_text text="--mate-pair" />
94 <has_text text="--no_overhang" />
95 </assert_command>
96 <output name="output_log" file="shortreads/process_shortreads.out" compare="sim_size"/>
97 <output_collection name="demultiplexed_paired" type="list:paired" count="40">
98 <element name="PopA_01">
99 <element name="forward" value="shortreads/PopA_01.forward.fq.gz" ftype="fastqsanger.gz" compare="sim_size"/>
100 <element name="reverse" value="shortreads/PopA_01.reverse.fq.gz" ftype="fastqsanger.gz" compare="sim_size"/>
101 </element>
102 </output_collection>
103 <output_collection name="remaining" type="list:paired" count="40">
104 <element name="PopA_01">
105 <element name="forward" file="shortreads/PopA_01.rem.forward.fq.gz" ftype="fastqsanger.gz"/>
106 <element name="reverse" file="shortreads/PopA_01.rem.reverse.fq.gz" ftype="fastqsanger.gz"/>
107 </element>
108 </output_collection>
109 <output_collection name="discarded_paired" type="list:paired" count="1">
110 <element name="reads">
111 <element name="forward" file="shortreads/reads.forward.fq" ftype="fastqsanger"/>
112 <element name="reverse" file="shortreads/reads.forward.fq" ftype="fastqsanger"/>
113 </element>
114 </output_collection>
115 </test>
116 </tests>
117 <help>
118 <![CDATA[
119 .. class:: infomark
120
121 **What it does**
122
123 Performs the same task as process_radtags for fast cleaning of randomly sheared genomic or transcriptomic data, not for RAD data.
124
125 **Help**
126
127 Input files:
128
129 - FASTQ
130
131 - Barcode File Format
132
133 The barcode file is a very simple format:
134
135 ======= ===========
136 Barcode Sample name
137 ======= ===========
138 ATGGGG PopA_01
139 GGGTAA PopA_02
140 AGGAAA PopA_03
141 TTTAAG PopA_04
142 GGTGTG PopA_05
143 TGATGT PopA_06
144 ======= ===========
145
146 Combinatorial barcodes are specified, one per column, separated by a tab:
147
148 ======== ======== ===========
149 Barcode1 Barcode2 Sample name
150 ======== ======== ===========
151 CGATA ACGTA PopA_01
152 CGGCG CGTA PopA_02
153 GAAGC CGTA PopA_03
154 GAGAT CGTA PopA_04
155 CGATA AGCA PopA_05
156 CGGCG AGCA PopA_06
157 ======== ======== ===========
158
159 @STACKS_INFOS@
160 ]]>
161 </help>
162 <expand macro="citation" />
163 </tool>