| Previous changeset 1:3ed9b8271977 (2021-04-15) |
|
Commit message:
Uploaded |
|
modified:
crispresso2.xml |
| b |
| diff -r 3ed9b8271977 -r eb5dbcfac76b crispresso2.xml --- a/crispresso2.xml Thu Apr 15 14:48:30 2021 +0000 +++ b/crispresso2.xml Thu May 05 14:45:06 2022 +0000 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="crispresso2" name="CRISPResso2" version="0.1.0" python_template_version="3.5"> +<tool id="crispresso2" name="CRISPResso2" version="0.1.1" python_template_version="3.5"> <requirements> <requirement type="package" version="2.0.45">crispresso2</requirement> </requirements> @@ -61,6 +61,12 @@ #if $filtering_parameters.max_paired_end_reads_overlap: --max_paired_end_reads_overlap $filtering_parameters.max_paired_end_reads_overlap #end if + #if $window_parameters.cleavage_offset: + --cleavage_offset '$window_parameters.cleavage_offset' + #end if + #if $output_parameters.suppress_report: + --suppress_report + #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}'/CRISPResso_on_reads/CRISPResso_quantification_of_editing_frequency.txt $quant_editing_freq @@ -100,8 +106,12 @@ <param argument="--max_paired_end_reads_overlap" type="integer" value="100" label="Maximum overlap length between reads" help="Parameter for the FLASH merging step. Maximum overlap length expected in approximately 90% of read pairs. Please see the FLASH manual for more information. (default: 100)"/> <param name="stringent_flash_merging" truevalue="--stringent_flash_merging" falsevalue="" type="boolean" default="False" label="Use stringent parameters for flash merging" help="In the case where flash could merge R1 and R2 reads ambiguously, the expected overlap is calculated as 2*average_read_length - amplicon_length. The flash parameters for --min-overlap and --max-overlap will be set to prefer merged reads with length within 10bp of the expected overlap. These values override the --min_paired_end_reads_overlap or --max_paired_end_reads_overlap CRISPResso parameters"/> </section> - <!--<section name="window_parameters" expanded="false" title="Quantification window parameters">--> - <!--</section>--> + <section name="window_parameters" expanded="false" title="Quantification window parameters"> + <param argument="cleavage_offset" type="integer" optional="True" default="-3" label="Center of quantification window to use within respect to the 3' end of the provided sgRNA sequence." help="-wc or --quantification_window_center or --cleavage_offset (default = -3)"/> + </section> + <section name="output_parameters" expanded="false" title="Output parameters"> + <param name="suppress_report" type="boolean" default="False" label="Suppress output report, plots output as .pdf only (not .png)" help="--suppress_report"/> + </section> </inputs> <outputs> <data format="txt" name="output_log" label="${tool.name} on ${on_string}: log" from_work_dir="Log.final.out"/> |