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1 <tool id="crispresso2" name="CRISPResso2" version="0.1.0" python_template_version="3.5">
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2 <requirements>
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3 <requirement type="package" version="2.0.45">crispresso2</requirement>
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4 </requirements>
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5 <command detect_errors="exit_code"><![CDATA[
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6 mkdir crispresso_out;
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7 #if $singlePaired.fastq_r1.is_of_type('fastq.gz', 'fastqsanger.gz'):
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8 #set $r1 = 'seq_name.fastq.gz'
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9 #else:
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10 #set $r1 = 'seq_name.fastq'
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11 #end if
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12 ln -s $singlePaired.fastq_r1 $r1;
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13 mkdir -p '${html_file.files_path}' &&
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14 #if str($singlePaired.sPaired) == 'paired':
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15 #if $singlePaired.fastq_r2.is_of_type('fastq.gz', 'fastqsanger.gz'):
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1
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16 #set $r2 = 'seq_name2.fastq.gz'
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0
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17 #else:
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1
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18 #set $r2 = 'seq_name2.fastq'
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19 #end if
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20 ln -s $singlePaired.fastq_r2 $r2;
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21 #end if
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22 CRISPResso --fastq_r1 $r1
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23 #if str($singlePaired.sPaired) == 'paired':
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24 --fastq_r2 $r2
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25 #end if
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26 --amplicon_seq '$amplicon_seq'
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27 -an '$amplicon_name'
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1
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28 -n reads
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29 #if $sgrna_parameters.guide_seq:
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30 --guide_seq $sgrna_parameters.guide_seq
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31 #end if
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0
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32 #if $sgrna_parameters.guide_name:
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33 --guide_name $sgrna_parameters.guide_name
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34 #end if
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35 #if $sgrna_parameters.flexiguide:
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36 -fg $sgrna_parameters.flexiguide
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37 #end if
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38 #if $sgrna_parameters.flexiguide_homology:
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39 --flexiguide_homology $sgrna_parameters.flexiguide_homology
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40 #end if
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41 #if $sgrna_parameters.flexiguide_name:
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42 --flexiguide_name '$sgrna_parameters.flexiguide_name'
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43 #end if
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44 #if $coding_seq:
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45 --coding_seq '$coding_seq'
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46 #end if
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47 $sgrna_parameters.discard_guide_positions_overhanging_amplicon_edge
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48 $filtering_parameters.split_interleaved_input
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49 #if $filtering_parameters.min_average_read_quality:
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50 --min_average_read_quality $filtering_parameters.min_average_read_quality
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51 #end if
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52 #if $filtering_parameters.min_single_bp_quality:
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53 --min_single_bp_quality $filtering_parameters.min_single_bp_quality
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54 #end if
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55 #if $filtering_parameters.min_bp_quality_or_N:
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56 --min_bp_quality_or_N $filtering_parameters.min_bp_quality_or_N
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57 #end if
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58 #if $filtering_parameters.min_paired_end_reads_overlap:
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59 --min_paired_end_reads_overlap $filtering_parameters.min_paired_end_reads_overlap
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60 #end if
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61 #if $filtering_parameters.max_paired_end_reads_overlap:
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62 --max_paired_end_reads_overlap $filtering_parameters.max_paired_end_reads_overlap
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63 #end if
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64 $filtering_parameters.stringent_flash_merging
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65 -o '${html_file.files_path}' > $output_log
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1
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66 && cp '${html_file.files_path}'/*\.html crispresso.html && cp '${html_file.files_path}'/CRISPResso_on_reads/CRISPResso_quantification_of_editing_frequency.txt $quant_editing_freq
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67 ]]></command>
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68 <inputs>
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69 <conditional name="singlePaired">
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70 <param name="sPaired" type="select" label="Single-end or paired-end reads">
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71 <option value="single" selected="true">Single-end</option>
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72 <option value="paired">Paired-end</option>
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73 </param>
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74 <when value="single">
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75 <param format="fastq,fastq.gz,fastqsanger.gz" name="fastq_r1" type="data" label="FASTQ file"/>
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76 </when>
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77 <when value="paired">
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78 <param format="fastq,fastq.gz,fastqsanger.gz" name="fastq_r1" type="data" label="FASTQ file, forward reads"/>
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79 <param format="fastq,fastq.gz,fastqsanger.gz" name="fastq_r2" type="data" label="FASTQ file, reverse reads"/>
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80 </when>
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81 </conditional>
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82 <param name="amplicon_seq" type="text" label="Amplicon sequence" help="If submitting more than 1 amplicon, use commas to separate them"/>
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83 <param name="amplicon_name" type="text" label="Amplicon name" help="--amplicon_name"/>
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84 <param name="expected_hdr_amplicon_seq" type="text" label="Amplicon sequence expected after HDR" help="--expected_hdr_amplicon_seq"/>
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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"/>
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86 <section name="sgrna_parameters" expanded="false" title="sgRNA parameters">
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87 <param argument="--guide_name" type="text" label="sgRNA names" help="if more than one, please separate by commas. (default: sgRNA)"/>
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1
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88 <param argument="--guide_seq" type="text" value="" label="sgRNA sequence" help="sgRNA sequence, if more than one, please separate by commas"/>
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89 <param argument="--flexiguide_name" type="text" value="" optional="True" label="Names for the flexiguides" help="Similar to --guide_name"/>
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0
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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"/>
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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)"/>
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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"/>
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93 </section>
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94 <section name="filtering_parameters" expanded="false" title="Read filtering, trimming, and merging parameters">
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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"/>
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96 <param argument="--min_average_read_quality" value="0" type="integer" label="Minimum average quality score (phred33) to keep a read"/>
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97 <param argument="--min_single_bp_quality" type="integer" value="0" label="Minimum single bp score (phred33) to keep a read"/>
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98 <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'"/>
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99 <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)" />
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100 <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)"/>
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101 <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"/>
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102 </section>
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103 <!--<section name="window_parameters" expanded="false" title="Quantification window parameters">-->
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104 <!--</section>-->
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105 </inputs>
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106 <outputs>
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107 <data format="txt" name="output_log" label="${tool.name} on ${on_string}: log" from_work_dir="Log.final.out"/>
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108 <data name="html_file" format="html" from_work_dir="crispresso.html" label="WebPage report"/>
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109 <data format="txt" name="quant_editing_freq" label="CRISPResso_quantification_of_editing_frequency"/>
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110 </outputs>
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111 <help><![CDATA[
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112 TODO: Fill in help.
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113 ]]></help>
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114 </tool>
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