Mercurial > repos > iuc > stacks2_shortreads

comparison stacks_shortreads.xml @ 2:43e3eeb2e0ec draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
author iuc
date Wed, 15 Jul 2020 17:42:30 -0400
parents 1974fee35ca7
children c5d7050e4ad7
comparison
equal deleted inserted replaced
1:1974fee35ca7 2:43e3eeb2e0ec
8 <expand macro="requirements"/> 8 <expand macro="requirements"/>
9 <expand macro="version_cmd"/> 9 <expand macro="version_cmd"/>
10 <command detect_errors="aggressive"><![CDATA[ 10 <command detect_errors="aggressive"><![CDATA[
11 @FASTQ_INPUT_FUNCTIONS@ 11 @FASTQ_INPUT_FUNCTIONS@
12 12
13 python '$__tool_directory__'/check_bcfile.py '$barcode' &&
14
13 mkdir stacks_inputs stacks_outputs && 15 mkdir stacks_inputs stacks_outputs &&
14
15 #if $output_log
16 ln -s '$output_log' stacks_outputs/process_shortreads.log &&
17 #end if
18 16
19 #set ($link_command, $inputype) = $fastq_input_nonbatch( $input_type.fqinputs, $input_type.input_type_select, "_R%d_0" ) 17 #set ($link_command, $inputype) = $fastq_input_nonbatch( $input_type.fqinputs, $input_type.input_type_select, "_R%d_0" )
20 $link_command 18 $link_command
21 19
22 20
38 36
39 <inputs> 37 <inputs>
40 <expand macro="fastq_input_bc_file" multiple="true" listtype="list:paired"/> 38 <expand macro="fastq_input_bc_file" multiple="true" listtype="list:paired"/>
41 <section name="options_advanced" title="advanced options" expanded="False"> 39 <section name="options_advanced" title="advanced options" expanded="False">
42 <expand macro="common_advanced"/> 40 <expand macro="common_advanced"/>
43 <param argument="--no_read_trimming" type="boolean" checked="false" truevalue="--no_read_trimming" falsevalue="" label="Do not trim low quality reads, just discard them" /> 41 <param argument="--no_read_trimming" type="boolean" checked="false" truevalue="--no_read_trimming" falsevalue="" label="Do not trim low quality reads, just discard them"/>
44 <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" /> 42 <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"/>
45 <param argument="--no_overhang" type="boolean" checked="false" truevalue="--no_overhang" falsevalue="" label="Data does not contain an overhang nucleotide between barcode and seqeunce" /> 43 <param argument="--no_overhang" type="boolean" checked="false" truevalue="--no_overhang" falsevalue="" label="Data does not contain an overhang nucleotide between barcode and seqeunce"/>
46 <expand macro="rescue_barcode"/> 44 <expand macro="rescue_barcode"/>
47 <expand macro="process_adapter"/> 45 <expand macro="process_adapter"/>
48 </section> 46 </section>
49 <expand macro="process_filter"/> 47 <expand macro="process_filter"/>
50 <expand macro="process_output_types"/> 48 <expand macro="process_output_types"/>
51 </inputs> 49 </inputs>
52 50
53 <outputs> 51 <outputs>
54 <data format="txt" name="output_log" label="${tool.name} on ${on_string} log file" from_work_dir="stacks_outputs/process_shortreads.log" /> 52 <data format="txt" name="output_log" label="${tool.name} on ${on_string} log file" from_work_dir="stacks_outputs/process_shortreads.log">
53 <filter>add_log</filter>
54 </data>
55 <expand macro="process_outputs"/> 55 <expand macro="process_outputs"/>
56 </outputs> 56 </outputs>
57 57
58 <tests> 58 <tests>
59 <!-- test single end, default options --> 59 <!-- test single end, default options -->
60 <test> 60 <test expect_num_outputs="2">
61 <param name="input_type|input_type_select" value="single"/> 61 <param name="input_type|input_type_select" value="single"/>
62 <param name="input_type|fqinputs" ftype="fastqsanger" value="procrad/R1.fq"/> 62 <param name="input_type|fqinputs" ftype="fastqsanger" value="procrad/R1.fq"/>
63 <param name="input_type|barcode_encoding" value="--inline_null"/> 63 <param name="input_type|barcode_encoding" value="--inline_null"/>
64 <param name="barcode" value="procrad/barcodes"/> 64 <param name="barcode" value="procrad/barcodes"/>
65 <param name="add_log" value="yes" /> 65 <param name="add_log" value="yes"/>
66 <output name="output_log" file="shortreads/process_shortreads.out" lines_diff="4"/> 66 <output name="output_log" file="shortreads/process_shortreads.out" lines_diff="4"/>
67 <output_collection name="demultiplexed" count="40"> 67 <output_collection name="demultiplexed" count="40">
68 <element name="PopA_01" file="shortreads/PopA_01.fq" ftype="fastqsanger" /> 68 <element name="PopA_01" file="shortreads/PopA_01.fq" ftype="fastqsanger"/>
69 </output_collection> 69 </output_collection>
70 </test> 70 </test>
71 <!-- test single end, default options --> 71 <!-- test single end, default options -->
72 <test> 72 <test expect_num_outputs="4">
73 <param name="input_type|input_type_select" value="paired"/> 73 <param name="input_type|input_type_select" value="paired"/>
74 <param name="input_type|fqinputs"> 74 <param name="input_type|fqinputs">
75 <collection type="list:paired"> 75 <collection type="list:paired">
76 <element name="reads"> 76 <element name="reads">
77 <collection type="paired"> 77 <collection type="paired">
78 <element name="forward" value="procrad/R1.fq" ftype="fastqsanger" /> 78 <element name="forward" value="procrad/R1.fq" ftype="fastqsanger"/>
79 <element name="reverse" value="procrad/R2.fq" ftype="fastqsanger"/> 79 <element name="reverse" value="procrad/R2.fq" ftype="fastqsanger"/>
80 </collection> 80 </collection>
81 </element> 81 </element>
82 </collection> 82 </collection>
83 </param> 83 </param>
84 <param name="input_type|barcode_encoding" value="--inline_null"/> 84 <param name="input_type|barcode_encoding" value="--inline_null"/>
85 <param name="barcode" value="procrad/barcodes"/> 85 <param name="barcode" value="procrad/barcodes"/>
86 <param name="capture" value="-D"/> 86 <param name="capture" value="-D"/>
87 <param name="no_read_trimming" value="--no_read_trimming" /> 87 <param name="no_read_trimming" value="--no_read_trimming"/>
88 <param name="mate_pair" value="--mate-pair" /> 88 <param name="mate_pair" value="--mate-pair"/>
89 <param name="no_overhang" value="--no_overhang" /> 89 <param name="no_overhang" value="--no_overhang"/>
90 <param name="outype" value="gzfastq"/> 90 <param name="outype" value="gzfastq"/>
91 <param name="add_log" value="yes" /> 91 <param name="add_log" value="yes"/>
92 <assert_command> 92 <assert_command>
93 <has_text text="-D" /> 93 <has_text text="-D"/>
94 <has_text text="--no_read_trimming" /> 94 <has_text text="--no_read_trimming"/>
95 <has_text text="--mate-pair" /> 95 <has_text text="--mate-pair"/>
96 <has_text text="--no_overhang" /> 96 <has_text text="--no_overhang"/>
97 </assert_command> 97 </assert_command>
98 <output name="output_log" file="shortreads/process_shortreads.out" compare="sim_size"/> 98 <output name="output_log">
99 <assert_contents><has_text text="ATGTAG"/></assert_contents>
100 <assert_contents><has_text text="Sequences not recorded"/></assert_contents>
101 </output>
99 <output_collection name="demultiplexed_paired" type="list:paired" count="40"> 102 <output_collection name="demultiplexed_paired" type="list:paired" count="40">
100 <element name="PopA_01"> 103 <element name="PopA_01">
101 <element name="forward" value="shortreads/PopA_01.forward.fq.gz" ftype="fastqsanger.gz" compare="sim_size"/> 104 <element name="forward" value="shortreads/PopA_01.forward.fq.gz" ftype="fastqsanger.gz" compare="sim_size" delta_frac="0.01"/>
102 <element name="reverse" value="shortreads/PopA_01.reverse.fq.gz" ftype="fastqsanger.gz" compare="sim_size"/> 105 <element name="reverse" value="shortreads/PopA_01.reverse.fq.gz" ftype="fastqsanger.gz" compare="sim_size" delta_frac="0.01"/>
103 </element> 106 </element>
104 </output_collection> 107 </output_collection>
105 <output_collection name="remaining" type="list:paired" count="40"> 108 <output_collection name="remaining" type="list:paired" count="40">
106 <element name="PopA_01"> 109 <element name="PopA_01">
107 <element name="forward" file="shortreads/PopA_01.rem.forward.fq.gz" ftype="fastqsanger.gz"/> 110 <element name="forward" file="shortreads/PopA_01.rem.forward.fq.gz" ftype="fastqsanger.gz"/>
159 ======== ======== =========== 162 ======== ======== ===========
160 163
161 @STACKS_INFOS@ 164 @STACKS_INFOS@
162 ]]> 165 ]]>
163 </help> 166 </help>
164 <expand macro="citation" /> 167 <expand macro="citation"/>
165 </tool> 168 </tool>