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comparison prinseq.xml @ 4:654b3a274ed5 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ commit 9cd78488b53cde8d3139d2d71ec500e2c91b9335"
author iuc
date Wed, 07 Jul 2021 09:22:27 +0000
parents 02befcb391f5
children 1ee282794de3
comparison
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3:02befcb391f5 4:654b3a274ed5
1 <tool id="prinseq" name="PRINSEQ" version="0.20.4"> 1 <tool id="prinseq" name="PRINSEQ" version="@TOOL_VERSION+galaxy1">
2 <description>to process quality of sequences</description> 2 <description>to process quality of sequences</description>
3 <macros>
4 <token name="@TOOL_VERSION">0.20.4</token>
5 </macros>
3 <requirements> 6 <requirements>
4 <requirement type="package" version="0.20.4">prinseq</requirement> 7 <requirement type="package" version="@TOOL_VERSION">prinseq</requirement>
5 </requirements> 8 </requirements>
6 9
7 <stdio> 10 <stdio>
8 <exit_code range="1:" level="fatal" description="" /> 11 <exit_code range="1:" level="fatal" description="" />
9 <regex match="ERROR" 12 <regex match="ERROR"
32 #if $seq_type.seq_type_opt == "single": 35 #if $seq_type.seq_type_opt == "single":
33 -fastq '$seq_type.input_singles' 36 -fastq '$seq_type.input_singles'
34 #if $seq_type.input_singles.is_of_type('fastqillumina'): 37 #if $seq_type.input_singles.is_of_type('fastqillumina'):
35 -phred64 38 -phred64
36 #end if 39 #end if
37 #else: 40 #elif $seq_type.seq_type_opt == "paired":
38 -fastq '$seq_type.input_mate1' 41 -fastq '$seq_type.input_mate1'
39 -fastq2 '$seq_type.input_mate2' 42 -fastq2 '$seq_type.input_mate2'
40 #if $seq_type.input_mate1.ext != $seq_type.input_mate2.ext: 43 #if $seq_type.input_mate1.ext != $seq_type.input_mate2.ext:
41 #import sys 44 #import sys
42 #silent sys.stderr.write( 'Both pairs from your paired-end library need to be from the same filetype.' ) 45 #silent sys.stderr.write( 'Both pairs from your paired-end library need to be from the same filetype.' )
43 #end if 46 #end if
44 #if $seq_type.input_mate1.is_of_type('fastqillumina'): 47 #if $seq_type.input_mate1.is_of_type('fastqillumina'):
48 -phred64
49 #end if
50 #else
51 -fastq '$seq_type.input_collection.forward'
52 -fastq2 '$seq_type.input_collection.reverse'
53 #if $seq_type.input_collection.forward.is_of_type('fastqillumina'):
45 -phred64 54 -phred64
46 #end if 55 #end if
47 #end if 56 #end if
48 57
49 -out_good "tmp/good_sequences" 58 -out_good "tmp/good_sequences"
223 <inputs> 232 <inputs>
224 <conditional name="seq_type"> 233 <conditional name="seq_type">
225 <param name="seq_type_opt" type="select" label="Is this library paired- or single-end?"> 234 <param name="seq_type_opt" type="select" label="Is this library paired- or single-end?">
226 <option value="single" selected="true">Single-end</option> 235 <option value="single" selected="true">Single-end</option>
227 <option value="paired">Paired-end</option> 236 <option value="paired">Paired-end</option>
237 <option value="paired_collection">Paired Collection</option>
228 </param> 238 </param>
229 <when value="single"> 239 <when value="single">
230 <param name="input_singles" type="data" format="fastqsanger,fastqillumina,fastq" label="FASTQ file" help="FASTQ files." /> 240 <param name="input_singles" type="data" format="fastqsanger,fastqillumina,fastq" label="FASTQ file" help="FASTQ files." />
231 </when> 241 </when>
232 <when value="paired"> 242 <when value="paired">
233 <param name="input_mate1" type="data" format="fastqsanger,fastqillumina,fastq" label="FASTQ file" help="FASTQ files." /> 243 <param name="input_mate1" type="data" format="fastqsanger,fastqillumina,fastq" label="FASTQ file" help="FASTQ files." />
234 <param name="input_mate2" type="data" format="fastqsanger,fastqillumina,fastq" label="FASTQ file" help="FASTQ files." /> 244 <param name="input_mate2" type="data" format="fastqsanger,fastqillumina,fastq" label="FASTQ file" help="FASTQ files." />
245 </when>
246 <when value="paired_collection">
247 <param name="input_collection" type="data_collection" collection_type="paired" label="FASTQ collection" help="FASTQ data in a paired collection" />
235 </when> 248 </when>
236 </conditional> 249 </conditional>
237 250
238 <conditional name="filter_treatments"> 251 <conditional name="filter_treatments">
239 <param name="apply_filter_treatments" type="select" label="Apply filter treatments?"> 252 <param name="apply_filter_treatments" type="select" label="Apply filter treatments?">
648 </data> 661 </data>
649 <data format_source="input_mate2" name="rejected_sequence_2_file" from_work_dir="tmp/rejected_sequences_2.fastq" 662 <data format_source="input_mate2" name="rejected_sequence_2_file" from_work_dir="tmp/rejected_sequences_2.fastq"
650 label="${tool.name} on ${on_string}: Rejected sequences for R2" > 663 label="${tool.name} on ${on_string}: Rejected sequences for R2" >
651 <filter>seq_type['seq_type_opt'] == "paired"</filter> 664 <filter>seq_type['seq_type_opt'] == "paired"</filter>
652 </data> 665 </data>
666
667 <collection name="good_sequences_collection" type="paired">
668 <filter>seq_type['seq_type_opt'] == "paired_collection"</filter>
669 </collection>
670
671 <collection name="singletons_collection" type="paired">
672 <filter>seq_type['seq_type_opt'] == "paired_collection"</filter>
673 </collection>
674
675 <collection name="rejected_sequences_collection" type="paired">
676 <filter>seq_type['seq_type_opt'] == "paired_collection"</filter>
677 </collection>
653 678
654 <!--<data format="html" name="html_file" from_work_dir="stats_html.html" 679 <!--<data format="html" name="html_file" from_work_dir="stats_html.html"
655 label="${tool.name} on ${on_string}: Summary" />--> 680 label="${tool.name} on ${on_string}: Summary" />-->
656 </outputs> 681 </outputs>
657 682