| Next changeset 1:3ed9b8271977 (2021-04-15) |
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Commit message:
Uploaded |
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added:
.shed.yml crispresso2.xml |
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| diff -r 000000000000 -r a378f3ee0137 .shed.yml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/.shed.yml Thu Mar 25 14:03:59 2021 +0000 |
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| @@ -0,0 +1,14 @@ +categories: + - Sequence Analysis +description: | + CRISPResso2 is a software pipeline designed to enable rapid and intuitive interpretation of genome editing experiments +long_description: | + CRISPResso2 + 1) Aligns sequencing reads to a reference sequence + 2) Quantifies insertions, mutations and deletions to determine whether a read is modified or unmodified by genome editing + 3) summarizes editing results in intuitive plots and datasets +name: crispresso2 +owner: iuc +remote_repository_url: https://github.com/ieguinoa/CRISPResso2_wrapper +homepage_url: https://github.com/pinellolab/CRISPResso2 +type: unrestricted |
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| diff -r 000000000000 -r a378f3ee0137 crispresso2.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/crispresso2.xml Thu Mar 25 14:03:59 2021 +0000 |
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| b'@@ -0,0 +1,110 @@\n+<tool id="crispresso2" name="CRISPResso2" version="0.1.0" python_template_version="3.5">\n+ <requirements>\n+ <requirement type="package" version="2.0.45">crispresso2</requirement>\n+ </requirements>\n+ <command detect_errors="exit_code"><![CDATA[\n+ mkdir crispresso_out;\n+ #if $singlePaired.fastq_r1.is_of_type(\'fastq.gz\', \'fastqsanger.gz\'):\n+ #set $r1 = \'seq_name.fastq.gz\'\n+ #else:\n+ #set $r1 = \'seq_name.fastq\'\n+ #end if\n+ ln -s $singlePaired.fastq_r1 $r1;\n+ mkdir -p \'${html_file.files_path}\' &&\n+ #if str($singlePaired.sPaired) == \'paired\':\n+ #if $singlePaired.fastq_r2.is_of_type(\'fastq.gz\', \'fastqsanger.gz\'):\n+ #set $r2 = \'seq_name.fastq.gz\'\n+ #else:\n+ #set $r2 = \'seq_name.fastq\'\n+ #end if\n+ ln -s $singlePaired.fastq_r2 $r2;\n+ #end if\n+ CRISPResso --fastq_r1 $r1\n+ #if str($singlePaired.sPaired) == \'paired\':\n+ --fastq_r2 $r2\n+ #end if\n+ --amplicon_seq \'$amplicon_seq\' \n+ -an \'$amplicon_name\'\n+ -n output\n+ #if $sgrna_parameters.guide_name:\n+ --guide_name $sgrna_parameters.guide_name\n+ #end if\n+ #if $sgrna_parameters.flexiguide:\n+ -fg $sgrna_parameters.flexiguide\n+ #end if\n+ #if $sgrna_parameters.flexiguide_homology:\n+ --flexiguide_homology $sgrna_parameters.flexiguide_homology\n+ #end if\n+ #if $sgrna_parameters.flexiguide_name:\n+ --flexiguide_name \'$sgrna_parameters.flexiguide_name\'\n+ #end if\n+ #if $coding_seq:\n+ --coding_seq \'$coding_seq\'\n+ #end if\n+ $sgrna_parameters.discard_guide_positions_overhanging_amplicon_edge\n+ $filtering_parameters.split_interleaved_input\n+ #if $filtering_parameters.min_average_read_quality:\n+ --min_average_read_quality $filtering_parameters.min_average_read_quality\n+ #end if\n+ #if $filtering_parameters.min_single_bp_quality:\n+ --min_single_bp_quality $filtering_parameters.min_single_bp_quality\n+ #end if\n+ #if $filtering_parameters.min_bp_quality_or_N:\n+ --min_bp_quality_or_N $filtering_parameters.min_bp_quality_or_N\n+ #end if\n+ #if $filtering_parameters.min_paired_end_reads_overlap:\n+ --min_paired_end_reads_overlap $filtering_parameters.min_paired_end_reads_overlap\n+ #end if\n+ #if $filtering_parameters.max_paired_end_reads_overlap:\n+ --max_paired_end_reads_overlap $filtering_parameters.max_paired_end_reads_overlap\n+ #end if\n+ $filtering_parameters.stringent_flash_merging\n+ -o \'${html_file.files_path}\' > $output_log \n+ && cp \'${html_file.files_path}\'/*\\.html crispresso.html\n+ ]]></command>\n+ <inputs>\n+ <conditional name="singlePaired">\n+ <param name="sPaired" type="select" label="Single-end or paired-end reads">\n+ <option value="single" selected="true">Single-end</option>\n+ <option value="paired">Paired-end</option>\n+ </param>\n+ <when value="single">\n+ <param format="fastq,fastq.gz,fastqsanger.gz" name="fastq_r1" type="data" label="FASTQ file"/>\n+ </when>\n+ <when value="paired">\n+ <param format="fastq,fastq.gz,fastqsanger.gz" name="fastq_r1" type="data" label="FASTQ file, forward reads"/>\n+ <param format="fastq,fastq.gz,fastqsanger.gz" name="fastq_r2" type="data" label="FASTQ file, reverse reads"/>\n+ </when>\n+ </conditional>\n+ <param name="amplicon_seq" type="text" label="Amplicon sequence" help="If submitting more than 1 amplicon, use commas to separate them"/>\n+ <param name="amplicon_name" type="text" label="Amplicon name" help="--amplicon_name"/>\n+ <param name="expected_hdr_amplicon_seq" type="text" label="Amp'..b'g_seq" type="text" value="" label="Subsequence/s of the amplicon sequence covering one or more coding sequences for frameshift analysis" help="--coding_seq"/>\n+ <section name="sgrna_parameters" expanded="false" title="sgRNA parameters">\n+ <param argument="--guide_name" type="text" label="sgRNA names" help="if more than one, please separate by commas. (default: sgRNA)"/>\n+ <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"/>\n+ <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)"/>\n+\n+ <param argument="--flexiguide_name" type="text" value="" optional="True" label="Names for the flexiguides" help="Similar to --guide_name"/>\n+ <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"/>\n+ </section>\n+ <section name="filtering_parameters" expanded="false" title="Read filtering, trimming, and merging parameters">\n+ <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"/>\n+ <param argument="--min_average_read_quality" value="0" type="integer" label="Minimum average quality score (phred33) to keep a read"/>\n+ <param argument="--min_single_bp_quality" type="integer" value="0" label="Minimum single bp score (phred33) to keep a read"/>\n+ <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\'"/>\n+ <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)" />\n+ <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)"/>\n+ <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"/>\n+ </section>\n+ <!--<section name="window_parameters" expanded="false" title="Quantification window parameters">-->\n+ <!--</section>-->\n+ </inputs>\n+ <outputs>\n+ <data format="txt" name="output_log" label="${tool.name} on ${on_string}: log" from_work_dir="Log.final.out"/>\n+ <data name="html_file" format="html" from_work_dir="crispresso.html" label="WebPage report"/>\n+ </outputs>\n+ <help><![CDATA[\n+ TODO: Fill in help.\n+ ]]></help>\n+</tool>\n' |