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comparison fastp.xml @ 4:7c82cb2a90c4 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 761a954744119f6317afe28eb50bd4f3fdea4984
author iuc
date Wed, 08 Aug 2018 08:49:26 -0400
parents e0b44bf2543e
children 3e2551a37201
comparison
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3:e0b44bf2543e 4:7c82cb2a90c4
1 <tool id="fastp" name="fastp" version="@WRAPPER_VERSION@.0"> 1 <tool id="fastp" name="fastp" version="@WRAPPER_VERSION@.1">
2 <description>- fast all-in-one preprocessing for FASTQ files</description> 2 <description>- fast all-in-one preprocessing for FASTQ files</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
7 <requirement type="package" version="@WRAPPER_VERSION@">fastp</requirement> 7 <requirement type="package" version="@WRAPPER_VERSION@">fastp</requirement>
8 </requirements> 8 </requirements>
9 <version_command>fastp -v</version_command> 9 <version_command>fastp -v</version_command>
10 <command detect_errors="exit_code"><![CDATA[ 10 <command detect_errors="exit_code"><![CDATA[
11 #import re
12
11 ## Link input files 13 ## Link input files
12 14
13 #if $in1.is_of_type('fastq.gz') 15 #if $in1.is_of_type('fastq.gz')
14 #set ext = 'fastq.gz' 16 #set ext = '.fastq.gz'
15 #else 17 #else
16 #set ext = 'fastq' 18 #set ext = '.fastq'
17 #end if 19 #end if
18 20
19 ln -s '$in1' input1.$ext && 21 #set $in1_name = re.sub('[^\w\-\s]', '_', str($in1.element_identifier)) + $ext
22 ln -s '$in1' $in1_name &&
20 23
21 #if str($single_paired.single_paired_selector) == 'paired': 24 #if str($single_paired.single_paired_selector) == 'paired':
22 ln -s '$in2' input2.$ext && 25 #set $in2_name = re.sub('[^\w\-\s]', '_', str($in2.element_identifier)) + $ext
23 #end if 26 ln -s '$in2' $in2_name &&
24 27 #end if
25
26 ## Set filename for output report
27
28 #import re
29 #set $filename = re.sub('[^\w\-\s]', '_', str($in1.element_identifier))
30 28
31 29
32 ## Run fastp 30 ## Run fastp
33 31
34 fastp 32 fastp
35 33
36 --thread \${GALAXY_SLOTS:-1} 34 --thread \${GALAXY_SLOTS:-1}
37 --report_title 'fastp report for $filename' 35 --report_title 'fastp report for $in1_name'
38 36
39 #if $in1.is_of_type('fastqillumina', 'fastqsolexa', 'fastqillumina.gz', 'fastqsolexa.gz'): 37 #if $in1.is_of_type('fastqillumina', 'fastqsolexa', 'fastqillumina.gz', 'fastqsolexa.gz'):
40 --phred64 38 --phred64
41 #end if 39 #end if
42 40
43 -i input1.$ext 41 -i $in1_name
44 -o first.$ext 42 -o first${ext}
45 43
46 #if str($single_paired.single_paired_selector) == 'paired': 44 #if str($single_paired.single_paired_selector) == 'paired':
47 -I input2.$ext 45 -I $in2_name
48 -O second.$ext 46 -O second${ext}
49 #end if 47 #end if
50 48
51 49
52 ## Adapter Trimming Options 50 ## Adapter Trimming Options
53 51
182 180
183 $read_mod_options.base_correction_options.correction 181 $read_mod_options.base_correction_options.correction
184 182
185 && 183 &&
186 184
187 mv first.$ext '${out1}' 185 mv first${ext} '${out1}'
188 #if str($single_paired.single_paired_selector) == 'paired': 186 #if str($single_paired.single_paired_selector) == 'paired':
189 && 187 &&
190 mv second.$ext '${out2}' 188 mv second${ext} '${out2}'
191 #end if 189 #end if
192 ]]></command> 190 ]]></command>
193 <inputs> 191 <inputs>
194 192
195 <conditional name="single_paired"> 193 <conditional name="single_paired">
307 </section> 305 </section>
308 </section> 306 </section>
309 307
310 <section name="output_options" title="Output Options" expanded="False"> 308 <section name="output_options" title="Output Options" expanded="False">
311 <param name="report_html" type="boolean" truevalue="True" falsevalue="False" checked="True" label="Output HTML report" help="fastp provides a QC report for the data Before and After filtering within a single HTML page, which enables comparison of the quality statistics changed by the preprocessing step directly"/> 309 <param name="report_html" type="boolean" truevalue="True" falsevalue="False" checked="True" label="Output HTML report" help="fastp provides a QC report for the data Before and After filtering within a single HTML page, which enables comparison of the quality statistics changed by the preprocessing step directly"/>
312 <param name="report_json" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Output JSON report" help="The JSON report contains all the data visualized in the HTML report. The format of the JSON report is manually optimized to be easily readable by humans"/> 310 <param name="report_json" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Output JSON report" help="The JSON report contains all the data visualized in the HTML report. The format of the JSON report is manually optimized to be easily readable by humans and is compatible with MultiQC"/>
313 </section> 311 </section>
314 </inputs> 312 </inputs>
315 313
316 <outputs> 314 <outputs>
317 <data name="out1" format_source="in1" label="${tool.name} on ${on_string}: Read 1 Output"/> 315 <data name="out1" format_source="in1" label="${tool.name} on ${on_string}: Read 1 Output"/>
467 * Processed reads 465 * Processed reads
468 466
469 Optionally, under **Output Options** you can choose to output 467 Optionally, under **Output Options** you can choose to output
470 468
471 * HTML report (default is Yes) 469 * HTML report (default is Yes)
472 * JSON report 470 * JSON report (compatible with MultiQC)
473 471
474 .. _fastp: https://github.com/OpenGene/fastp 472 .. _fastp: https://github.com/OpenGene/fastp
475 473
476 ]]></help> 474 ]]></help>
477 <citations> 475 <citations>