| Previous changeset 0:a378f3ee0137 (2021-03-25) Next changeset 2:eb5dbcfac76b (2022-05-05) |
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crispresso2.xml |
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| diff -r a378f3ee0137 -r 3ed9b8271977 crispresso2.xml --- a/crispresso2.xml Thu Mar 25 14:03:59 2021 +0000 +++ b/crispresso2.xml Thu Apr 15 14:48:30 2021 +0000 |
| [ |
| @@ -13,9 +13,9 @@ mkdir -p '${html_file.files_path}' && #if str($singlePaired.sPaired) == 'paired': #if $singlePaired.fastq_r2.is_of_type('fastq.gz', 'fastqsanger.gz'): - #set $r2 = 'seq_name.fastq.gz' + #set $r2 = 'seq_name2.fastq.gz' #else: - #set $r2 = 'seq_name.fastq' + #set $r2 = 'seq_name2.fastq' #end if ln -s $singlePaired.fastq_r2 $r2; #end if @@ -25,7 +25,10 @@ #end if --amplicon_seq '$amplicon_seq' -an '$amplicon_name' - -n output + -n reads + #if $sgrna_parameters.guide_seq: + --guide_seq $sgrna_parameters.guide_seq + #end if #if $sgrna_parameters.guide_name: --guide_name $sgrna_parameters.guide_name #end if @@ -60,7 +63,7 @@ #end if $filtering_parameters.stringent_flash_merging -o '${html_file.files_path}' > $output_log - && cp '${html_file.files_path}'/*\.html crispresso.html + && 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 ]]></command> <inputs> <conditional name="singlePaired"> @@ -82,10 +85,10 @@ <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"/> <section name="sgrna_parameters" expanded="false" title="sgRNA parameters"> <param argument="--guide_name" type="text" label="sgRNA names" help="if more than one, please separate by commas. (default: sgRNA)"/> + <param argument="--guide_seq" type="text" value="" label="sgRNA sequence" help="sgRNA sequence, if more than one, please separate by commas"/> + <param argument="--flexiguide_name" type="text" value="" optional="True" label="Names for the flexiguides" help="Similar to --guide_name"/> <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"/> <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)"/> - - <param argument="--flexiguide_name" type="text" value="" optional="True" label="Names for the flexiguides" help="Similar to --guide_name"/> <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"/> </section> <section name="filtering_parameters" expanded="false" title="Read filtering, trimming, and merging parameters"> @@ -103,6 +106,7 @@ <outputs> <data format="txt" name="output_log" label="${tool.name} on ${on_string}: log" from_work_dir="Log.final.out"/> <data name="html_file" format="html" from_work_dir="crispresso.html" label="WebPage report"/> + <data format="txt" name="quant_editing_freq" label="CRISPResso_quantification_of_editing_frequency"/> </outputs> <help><![CDATA[ TODO: Fill in help. |