Mercurial > repos > iuc > stacks2_shortreads
comparison stacks_shortreads.xml @ 0:ad7a60726fc3 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
author | iuc |
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date | Mon, 01 Jul 2019 11:02:39 -0400 |
parents | |
children | 1974fee35ca7 |
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-1:000000000000 | 0:ad7a60726fc3 |
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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> |