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comparison crispresso2.xml @ 0:a378f3ee0137 draft

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author ieguinoa
date Thu, 25 Mar 2021 14:03:59 +0000
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children 3ed9b8271977
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1 <tool id="crispresso2" name="CRISPResso2" version="0.1.0" python_template_version="3.5">
2 <requirements>
3 <requirement type="package" version="2.0.45">crispresso2</requirement>
4 </requirements>
5 <command detect_errors="exit_code"><![CDATA[
6 mkdir crispresso_out;
7 #if $singlePaired.fastq_r1.is_of_type('fastq.gz', 'fastqsanger.gz'):
8 #set $r1 = 'seq_name.fastq.gz'
9 #else:
10 #set $r1 = 'seq_name.fastq'
11 #end if
12 ln -s $singlePaired.fastq_r1 $r1;
13 mkdir -p '${html_file.files_path}' &&
14 #if str($singlePaired.sPaired) == 'paired':
15 #if $singlePaired.fastq_r2.is_of_type('fastq.gz', 'fastqsanger.gz'):
16 #set $r2 = 'seq_name.fastq.gz'
17 #else:
18 #set $r2 = 'seq_name.fastq'
19 #end if
20 ln -s $singlePaired.fastq_r2 $r2;
21 #end if
22 CRISPResso --fastq_r1 $r1
23 #if str($singlePaired.sPaired) == 'paired':
24 --fastq_r2 $r2
25 #end if
26 --amplicon_seq '$amplicon_seq'
27 -an '$amplicon_name'
28 -n output
29 #if $sgrna_parameters.guide_name:
30 --guide_name $sgrna_parameters.guide_name
31 #end if
32 #if $sgrna_parameters.flexiguide:
33 -fg $sgrna_parameters.flexiguide
34 #end if
35 #if $sgrna_parameters.flexiguide_homology:
36 --flexiguide_homology $sgrna_parameters.flexiguide_homology
37 #end if
38 #if $sgrna_parameters.flexiguide_name:
39 --flexiguide_name '$sgrna_parameters.flexiguide_name'
40 #end if
41 #if $coding_seq:
42 --coding_seq '$coding_seq'
43 #end if
44 $sgrna_parameters.discard_guide_positions_overhanging_amplicon_edge
45 $filtering_parameters.split_interleaved_input
46 #if $filtering_parameters.min_average_read_quality:
47 --min_average_read_quality $filtering_parameters.min_average_read_quality
48 #end if
49 #if $filtering_parameters.min_single_bp_quality:
50 --min_single_bp_quality $filtering_parameters.min_single_bp_quality
51 #end if
52 #if $filtering_parameters.min_bp_quality_or_N:
53 --min_bp_quality_or_N $filtering_parameters.min_bp_quality_or_N
54 #end if
55 #if $filtering_parameters.min_paired_end_reads_overlap:
56 --min_paired_end_reads_overlap $filtering_parameters.min_paired_end_reads_overlap
57 #end if
58 #if $filtering_parameters.max_paired_end_reads_overlap:
59 --max_paired_end_reads_overlap $filtering_parameters.max_paired_end_reads_overlap
60 #end if
61 $filtering_parameters.stringent_flash_merging
62 -o '${html_file.files_path}' > $output_log
63 && cp '${html_file.files_path}'/*\.html crispresso.html
64 ]]></command>
65 <inputs>
66 <conditional name="singlePaired">
67 <param name="sPaired" type="select" label="Single-end or paired-end reads">
68 <option value="single" selected="true">Single-end</option>
69 <option value="paired">Paired-end</option>
70 </param>
71 <when value="single">
72 <param format="fastq,fastq.gz,fastqsanger.gz" name="fastq_r1" type="data" label="FASTQ file"/>
73 </when>
74 <when value="paired">
75 <param format="fastq,fastq.gz,fastqsanger.gz" name="fastq_r1" type="data" label="FASTQ file, forward reads"/>
76 <param format="fastq,fastq.gz,fastqsanger.gz" name="fastq_r2" type="data" label="FASTQ file, reverse reads"/>
77 </when>
78 </conditional>
79 <param name="amplicon_seq" type="text" label="Amplicon sequence" help="If submitting more than 1 amplicon, use commas to separate them"/>
80 <param name="amplicon_name" type="text" label="Amplicon name" help="--amplicon_name"/>
81 <param name="expected_hdr_amplicon_seq" type="text" label="Amplicon sequence expected after HDR" help="--expected_hdr_amplicon_seq"/>
82 <param argument="--coding_seq" type="text" value="" label="Subsequence/s of the amplicon sequence covering one or more coding sequences for frameshift analysis" help="--coding_seq"/>
83 <section name="sgrna_parameters" expanded="false" title="sgRNA parameters">
84 <param argument="--guide_name" type="text" label="sgRNA names" help="if more than one, please separate by commas. (default: sgRNA)"/>
85 <param argument="--flexiguide" type="text" value="" label="sgRNA sequence (flexible)" help="The flexiguide sequence will be aligned to the amplicon sequence(s), as long as the guide sequence has homology as set by --flexiguide_homology"/>
86 <param argument="--flexiguide_homology" type="integer" value="80" label="Flexiguide homology" help="will yield guides in amplicons with at least this homology to the flexiguide sequence (default:80 meaning 80% homology is required)"/>
87
88 <param argument="--flexiguide_name" type="text" value="" optional="True" label="Names for the flexiguides" help="Similar to --guide_name"/>
89 <param name="discard_guide_positions_overhanging_amplicon_edge" truevalue="" falsevalue="--discard_guide_positions_overhanging_amplicon_edge" type="boolean" default="False" label="Discard guide positions overhanging amplicon edge" help="If set, for guides that align to multiple positions, guide positions will be discarded if plotting around those regions would included bp that extend beyond the end of the amplicon"/>
90 </section>
91 <section name="filtering_parameters" expanded="false" title="Read filtering, trimming, and merging parameters">
92 <param name="split_interleaved_input" type="boolean" default="False" truevalue="--split_interleaved_input" falsevalue="" label="Splits a single fastq file containing paired end reads in two files before running CRISPResso"/>
93 <param argument="--min_average_read_quality" value="0" type="integer" label="Minimum average quality score (phred33) to keep a read"/>
94 <param argument="--min_single_bp_quality" type="integer" value="0" label="Minimum single bp score (phred33) to keep a read"/>
95 <param argument="--min_bp_quality_or_N" type="integer" value="0" label="Bases with a quality score (phred33) less than this value will be set to 'N'"/>
96 <param argument="--min_paired_end_reads_overlap" type="integer" value="10" label="Minimum overlap length between reads" help="Parameter for the FLASH read merging step. Minimum required overlap length between two reads to provide a confident overlap. (default: 10)" />
97 <param argument="--max_paired_end_reads_overlap" type="integer" value="100" label="Maximum overlap length between reads" help="Parameter for the FLASH merging step. Maximum overlap length expected in approximately 90% of read pairs. Please see the FLASH manual for more information. (default: 100)"/>
98 <param name="stringent_flash_merging" truevalue="--stringent_flash_merging" falsevalue="" type="boolean" default="False" label="Use stringent parameters for flash merging" help="In the case where flash could merge R1 and R2 reads ambiguously, the expected overlap is calculated as 2*average_read_length - amplicon_length. The flash parameters for --min-overlap and --max-overlap will be set to prefer merged reads with length within 10bp of the expected overlap. These values override the --min_paired_end_reads_overlap or --max_paired_end_reads_overlap CRISPResso parameters"/>
99 </section>
100 <!--<section name="window_parameters" expanded="false" title="Quantification window parameters">-->
101 <!--</section>-->
102 </inputs>
103 <outputs>
104 <data format="txt" name="output_log" label="${tool.name} on ${on_string}: log" from_work_dir="Log.final.out"/>
105 <data name="html_file" format="html" from_work_dir="crispresso.html" label="WebPage report"/>
106 </outputs>
107 <help><![CDATA[
108 TODO: Fill in help.
109 ]]></help>
110 </tool>