Mercurial > repos > iuc > stacks2_sstacks

comparison macros_process.xml @ 2:0b8c84a7fdb5 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 17:20:51 -0400
parents e58e2ecb6285
children 09b8edb56d80
comparison
equal deleted inserted replaced
1:e58e2ecb6285 2:0b8c84a7fdb5
27 </param> 27 </param>
28 </xml> 28 </xml>
29 29
30 <xml name="discover_faqgz_output_macro" token_pattern="" token_dir=""> 30 <xml name="discover_faqgz_output_macro" token_pattern="" token_dir="">
31 <expand macro="discover_faq_output_macro" pattern="@PATTERN@" dir="@DIR@"/> 31 <expand macro="discover_faq_output_macro" pattern="@PATTERN@" dir="@DIR@"/>
32 <discover_datasets pattern="@PATTERN@\.fq\.gz$" ext="fastqsanger.gz" directory="@DIR@/" /> 32 <discover_datasets pattern="@PATTERN@\.fq\.gz$" ext="fastqsanger.gz" directory="@DIR@/"/>
33 <discover_datasets pattern="@PATTERN@\.fa\.gz$" ext="fasta.gz" directory="@DIR@/" /> 33 <discover_datasets pattern="@PATTERN@\.fa\.gz$" ext="fasta.gz" directory="@DIR@/"/>
34 </xml> 34 </xml>
35 <xml name="discover_faq_output_macro" token_pattern="" token_dir=""> 35 <xml name="discover_faq_output_macro" token_pattern="" token_dir="">
36 <discover_datasets pattern="@PATTERN@\.fq$" ext="fastqsanger" directory="@DIR@/" /> 36 <discover_datasets pattern="@PATTERN@\.fq$" ext="fastqsanger" directory="@DIR@/"/>
37 <discover_datasets pattern="@PATTERN@\.fa$" ext="fasta" directory="@DIR@/" /> 37 <discover_datasets pattern="@PATTERN@\.fa$" ext="fasta" directory="@DIR@/"/>
38 </xml> 38 </xml>
39 39
40 <xml name="process_outputs"> 40 <xml name="process_outputs">
41 <collection name="demultiplexed" type="list" label="${tool.name} on ${on_string} Demultiplexed reads"> 41 <collection name="demultiplexed" type="list" label="${tool.name} on ${on_string} Demultiplexed reads">
42 <filter>input_type['input_type_select'] == "single"</filter> 42 <filter>input_type['input_type_select'] == "single"</filter>
69 <param name="filter_select" type="select" label="Do quality filtering"> 69 <param name="filter_select" type="select" label="Do quality filtering">
70 <option value="yes">Yes</option> 70 <option value="yes">Yes</option>
71 <option value="no" selected="true">No</option> 71 <option value="no" selected="true">No</option>
72 </param> 72 </param>
73 <when value="yes"> 73 <when value="yes">
74 <param name="sliding" type="float" value="0.15" min="0" max="1" argument="-w" label="Set the size of the sliding window as a fraction of the read length, between 0 and 1" /> 74 <param name="sliding" type="float" value="0.15" min="0" max="1" argument="-w" label="Set the size of the sliding window as a fraction of the read length, between 0 and 1"/>
75 <param name="score" type="integer" value="10" min="0" max="40" argument="-s" label="Set the score limit. If the average score within the sliding window drops below this value, the read is discarded" /> 75 <param name="score" type="integer" value="10" min="0" max="40" argument="-s" label="Set the score limit. If the average score within the sliding window drops below this value, the read is discarded"/>
76 <param name="remove" type="boolean" checked="false" truevalue="-c" falsevalue="" argument="-c" label="Clean data, remove any read with an uncalled base" /> 76 <param name="remove" type="boolean" checked="false" truevalue="-c" falsevalue="" argument="-c" label="Clean data, remove any read with an uncalled base"/>
77 <param name="discard" type="boolean" checked="false" truevalue="-q" falsevalue="" argument="-q" label="Discard reads with low quality scores"/> 77 <param name="discard" type="boolean" checked="false" truevalue="-q" falsevalue="" argument="-q" label="Discard reads with low quality scores"/>
78 <param argument="--filter-illumina" name="filter_illumina" type="boolean" checked="false" truevalue="--filter-illumina" falsevalue="" label="Discard reads that have been marked by Illumina's chastity/purity filter as failing" /> 78 <param argument="--filter-illumina" name="filter_illumina" type="boolean" checked="false" truevalue="--filter-illumina" falsevalue="" label="Discard reads that have been marked by Illumina's chastity/purity filter as failing"/>
79 </when> 79 </when>
80 <when value="no"> 80 <when value="no">
81 <param argument="--len_limit" type="integer" value="" optional="true" label="Minimum sequence length" help="useful if your data has already been trimmed"/> 81 <param argument="--len_limit" type="integer" value="" optional="true" label="Minimum sequence length" help="useful if your data has already been trimmed"/>
82 </when> 82 </when>
83 </conditional> 83 </conditional>
84 <param name="capture" type="boolean" checked="false" truevalue="-D" falsevalue="" argument="-D" label="Capture discarded reads to a file" /> 84 <param name="capture" type="boolean" checked="false" truevalue="-D" falsevalue="" argument="-D" label="Capture discarded reads to a file"/>
85 </xml> 85 </xml>
86 <token name="@PROCESS_FILTER@"><![CDATA[ 86 <token name="@PROCESS_FILTER@"><![CDATA[
87 #if $filter_cond.filter_select == 'yes': 87 #if $filter_cond.filter_select == 'yes':
88 -w $filter_cond.sliding 88 -w $filter_cond.sliding
89 -s $filter_cond.score 89 -s $filter_cond.score
102 && mkdir stacks_outputs/discarded/ 102 && mkdir stacks_outputs/discarded/
103 && mv stacks_outputs/*discards stacks_outputs/discarded/ 103 && mv stacks_outputs/*discards stacks_outputs/discarded/
104 104
105 ## fix the _R[12]_0 that was added for preparing the input 105 ## fix the _R[12]_0 that was added for preparing the input
106 #if $input_type.input_type_select == 'paired': 106 #if $input_type.input_type_select == 'paired':
107 && find stacks_outputs/discarded/ -type f | while read file; do mv "\$file" "\$(echo \$file | sed 's/_R1_0/.1/; s/_R2_0/.2/;')"; done 107 && (find stacks_outputs/discarded/ -type f | while read file; do mv "\$file" "\$(echo \$file | sed 's/_R1_0/.1/; s/_R2_0/.2/;')"; done)
108 #end if 108 #end if
109 ## also remove the gz which is added by procrad (but its uncompressed) 109 ## also remove the gz which is added by procrad (but its uncompressed)
110 && find stacks_outputs/discarded/ -type f -iname "*.gz.discards" | while read file; do mv "\$file" "\$(echo \$file | sed 's/.gz.discards$/.discards/;')"; done 110 && (find stacks_outputs/discarded/ -type f -iname "*.gz.discards" | while read file; do mv "\$file" "\$(echo \$file | sed 's/.gz.discards$/.discards/;')"; done)
111 111
112 ## the discard files are named fastq even if the output is fasta 112 ## the discard files are named fastq even if the output is fasta
113 #if str($outype).endswith("fasta"): 113 #if str($outype).endswith("fasta"):
114 && find stacks_outputs/discarded/ -type f | while read file; do mv "\$file" "\$(echo \$file | sed 's/\.fastq.discards/.fa/;')"; done 114 && (find stacks_outputs/discarded/ -type f | while read file; do mv "\$file" "\$(echo \$file | sed 's/\.fastq.discards/.fa/;')"; done)
115 #else 115 #else
116 && find stacks_outputs/discarded/ -type f | while read file; do mv "\$file" "\$(echo \$file | sed 's/\.fastq.discards/.fq/;')"; done 116 && (find stacks_outputs/discarded/ -type f | while read file; do mv "\$file" "\$(echo \$file | sed 's/\.fastq.discards/.fq/;')"; done)
117 #end if 117 #end if
118 #end if 118 #end if
119 ## prepare paired read output for processing in galaxy 119 ## prepare paired read output for processing in galaxy
120 #if $input_type.input_type_select == 'paired': 120 #if $input_type.input_type_select == 'paired':
121 && mkdir stacks_outputs/remaining 121 && mkdir stacks_outputs/remaining
122 && find stacks_outputs -iregex ".*\.rem\.[12]\.f[aq]\(\.gz\)?" | while read file; do mv "\$file" stacks_outputs/remaining/; done 122 && (find stacks_outputs -iregex ".*\.rem\.[12]\.f[aq]\(\.gz\)?" | while read file; do mv "\$file" stacks_outputs/remaining/; done)
123 && find stacks_outputs/ -iregex ".*.f[aq]\(\.gz\)?" | while read file; do mv "\$file" "\$(echo \$file | sed 's/\.1\./.forward./; s/\.2\./.reverse./')"; done 123 && (find stacks_outputs/ -iregex ".*.f[aq]\(\.gz\)?" | while read file; do mv "\$file" "\$(echo \$file | sed 's/\.1\./.forward./; s/\.2\./.reverse./')"; done)
124 #end if 124 #end if
125 ]]></token> 125 ]]></token>
126 126
127 <!-- adapter trimming options --> 127 <!-- adapter trimming options -->
128 <xml name="process_adapter"> 128 <xml name="process_adapter">
129 <param argument="--adapter_1" type="text" value="" optional="true" label="Adaptor sequence that may occur on the first read" /> 129 <param argument="--adapter_1" type="text" value="" optional="true" label="Adaptor sequence that may occur on the first read"/>
130 <param argument="--adapter_2" type="text" value="" optional="true" label="Adaptor sequence that may occur on the paired-read" /> 130 <param argument="--adapter_2" type="text" value="" optional="true" label="Adaptor sequence that may occur on the paired-read"/>
131 <param argument="--adapter_mm" type="integer" value="" optional="true" label="Number of mismatches allowed in the adapter sequence"/> 131 <param argument="--adapter_mm" type="integer" value="" optional="true" label="Number of mismatches allowed in the adapter sequence"/>
132 </xml> 132 </xml>
133 <token name="@PROCESS_ADAPTER@"><![CDATA[ 133 <token name="@PROCESS_ADAPTER@"><![CDATA[
134 ## Adapter options 134 ## Adapter options
135 #if str($options_advanced.adapter_1) != "": 135 #if str($options_advanced.adapter_1) != "":
169 #end if 169 #end if
170 ]]></token> 170 ]]></token>
171 171
172 <!-- advanced options that are shared --> 172 <!-- advanced options that are shared -->
173 <xml name="common_advanced"> 173 <xml name="common_advanced">
174 <param name="truncate" type="integer" value="" optional="True" argument="-t" label="Truncate final read length to this value" /> 174 <param name="truncate" type="integer" value="" optional="True" argument="-t" label="Truncate final read length to this value"/>
175 <param argument="--retain_header" type="boolean" checked="false" truevalue="--retain_header" falsevalue="" label="Retain unmodified FASTQ headers in the output" /> 175 <param argument="--retain_header" type="boolean" checked="false" truevalue="--retain_header" falsevalue="" label="Retain unmodified FASTQ headers in the output"/>
176 </xml> 176 </xml>
177 <token name="@COMMON_ADVANCED@"><![CDATA[ 177 <token name="@COMMON_ADVANCED@"><![CDATA[
178 #if str($options_advanced.truncate) 178 #if str($options_advanced.truncate)
179 -t $options_advanced.truncate 179 -t $options_advanced.truncate
180 #end if 180 #end if
181 $options_advanced.retain_header 181 $options_advanced.retain_header
182 ]]></token> 182 ]]></token>
183 </macros> 183 </macros>
184