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comparison crispresso2.xml @ 1:3ed9b8271977 draft

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author ieguinoa
date Thu, 15 Apr 2021 14:48:30 +0000
parents a378f3ee0137
children eb5dbcfac76b
comparison
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0:a378f3ee0137 1:3ed9b8271977
11 #end if 11 #end if
12 ln -s $singlePaired.fastq_r1 $r1; 12 ln -s $singlePaired.fastq_r1 $r1;
13 mkdir -p '${html_file.files_path}' && 13 mkdir -p '${html_file.files_path}' &&
14 #if str($singlePaired.sPaired) == 'paired': 14 #if str($singlePaired.sPaired) == 'paired':
15 #if $singlePaired.fastq_r2.is_of_type('fastq.gz', 'fastqsanger.gz'): 15 #if $singlePaired.fastq_r2.is_of_type('fastq.gz', 'fastqsanger.gz'):
16 #set $r2 = 'seq_name.fastq.gz' 16 #set $r2 = 'seq_name2.fastq.gz'
17 #else: 17 #else:
18 #set $r2 = 'seq_name.fastq' 18 #set $r2 = 'seq_name2.fastq'
19 #end if 19 #end if
20 ln -s $singlePaired.fastq_r2 $r2; 20 ln -s $singlePaired.fastq_r2 $r2;
21 #end if 21 #end if
22 CRISPResso --fastq_r1 $r1 22 CRISPResso --fastq_r1 $r1
23 #if str($singlePaired.sPaired) == 'paired': 23 #if str($singlePaired.sPaired) == 'paired':
24 --fastq_r2 $r2 24 --fastq_r2 $r2
25 #end if 25 #end if
26 --amplicon_seq '$amplicon_seq' 26 --amplicon_seq '$amplicon_seq'
27 -an '$amplicon_name' 27 -an '$amplicon_name'
28 -n output 28 -n reads
29 #if $sgrna_parameters.guide_seq:
30 --guide_seq $sgrna_parameters.guide_seq
31 #end if
29 #if $sgrna_parameters.guide_name: 32 #if $sgrna_parameters.guide_name:
30 --guide_name $sgrna_parameters.guide_name 33 --guide_name $sgrna_parameters.guide_name
31 #end if 34 #end if
32 #if $sgrna_parameters.flexiguide: 35 #if $sgrna_parameters.flexiguide:
33 -fg $sgrna_parameters.flexiguide 36 -fg $sgrna_parameters.flexiguide
58 #if $filtering_parameters.max_paired_end_reads_overlap: 61 #if $filtering_parameters.max_paired_end_reads_overlap:
59 --max_paired_end_reads_overlap $filtering_parameters.max_paired_end_reads_overlap 62 --max_paired_end_reads_overlap $filtering_parameters.max_paired_end_reads_overlap
60 #end if 63 #end if
61 $filtering_parameters.stringent_flash_merging 64 $filtering_parameters.stringent_flash_merging
62 -o '${html_file.files_path}' > $output_log 65 -o '${html_file.files_path}' > $output_log
63 && cp '${html_file.files_path}'/*\.html crispresso.html 66 && cp '${html_file.files_path}'/*\.html crispresso.html && cp '${html_file.files_path}'/CRISPResso_on_reads/CRISPResso_quantification_of_editing_frequency.txt $quant_editing_freq
64 ]]></command> 67 ]]></command>
65 <inputs> 68 <inputs>
66 <conditional name="singlePaired"> 69 <conditional name="singlePaired">
67 <param name="sPaired" type="select" label="Single-end or paired-end reads"> 70 <param name="sPaired" type="select" label="Single-end or paired-end reads">
68 <option value="single" selected="true">Single-end</option> 71 <option value="single" selected="true">Single-end</option>
80 <param name="amplicon_name" type="text" label="Amplicon name" help="--amplicon_name"/> 83 <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"/> 84 <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"/> 85 <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"> 86 <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)"/> 87 <param argument="--guide_name" type="text" label="sgRNA names" help="if more than one, please separate by commas. (default: sgRNA)"/>
88 <param argument="--guide_seq" type="text" value="" label="sgRNA sequence" help="sgRNA sequence, if more than one, please separate by commas"/>
89 <param argument="--flexiguide_name" type="text" value="" optional="True" label="Names for the flexiguides" help="Similar to --guide_name"/>
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"/> 90 <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)"/> 91 <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"/> 92 <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> 93 </section>
91 <section name="filtering_parameters" expanded="false" title="Read filtering, trimming, and merging parameters"> 94 <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"/> 95 <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"/> 96 <param argument="--min_average_read_quality" value="0" type="integer" label="Minimum average quality score (phred33) to keep a read"/>
101 <!--</section>--> 104 <!--</section>-->
102 </inputs> 105 </inputs>
103 <outputs> 106 <outputs>
104 <data format="txt" name="output_log" label="${tool.name} on ${on_string}: log" from_work_dir="Log.final.out"/> 107 <data format="txt" name="output_log" label="${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"/> 108 <data name="html_file" format="html" from_work_dir="crispresso.html" label="WebPage report"/>
109 <data format="txt" name="quant_editing_freq" label="CRISPResso_quantification_of_editing_frequency"/>
106 </outputs> 110 </outputs>
107 <help><![CDATA[ 111 <help><![CDATA[
108 TODO: Fill in help. 112 TODO: Fill in help.
109 ]]></help> 113 ]]></help>
110 </tool> 114 </tool>