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author | iuc |
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date | Wed, 13 Mar 2024 14:12:11 +0000 |
parents | 7346619ad005 |
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<?xml version="1.0"?> <tool id="crispr_studio" name="CRISPR Studio" version="1+galaxy0"> <description> facilitate and accelerate CRISPR array visualization from a GFF3 file generated with CRISPRDetect </description> <xrefs> <xref type="bio.tools">crisprstudio</xref> </xrefs> <requirements> <requirement type="package" version="1">crispr_studio</requirement> </requirements> <command detect_errors="exit_code"> <![CDATA[ ln -s '${input_data}' ./infile && #if $rerun.r == '-r': ln -s '${rerun.prev_final}' infile.fasta_fasta36.spacermatch.mcl.final && ln -s '${rerun.prev_svg}' infile.fasta_fasta36.spacermatch.mcl.svg && #end if CRISPR_Studio #if $order.s_order == 'File': -l '${order.isolate_list}' #else: -s '${order.s_order}' #end if $f $n $gU $gS $rerun.r #if $cut_off: -c '${cut_off}' #end if -i ./infile ]]></command> <inputs> <param name="input_data" type="data" format="gff" label="Input sequences" help="gff (GFF3) files are valid"/> <conditional name="order"> <param name='s_order' type="select" label="Order of Isolates" help="Determine order of isolates in figure (-s)"> <option value="DistMatrix" selected="True">DistMatrix (Order extracted from a distance matrix based on the similarity of the arrays in the isolates.)</option> <option value="CRISPRDetect">CRISPRDetect (Order in GFF File)</option> <option value="File">By File</option> </param> <when value="DistMatrix"> </when> <when value="CRISPRDetect"> </when> <when value="File"> <param name="isolate_list" type="data" format="txt" optional="true" label="List of Isolates to show" help="Generate the figure with the subset of isolates listed in the file"/> </when> </conditional> <param argument="-n" truevalue="-n" falsevalue="" type="boolean" label="Show the size of the spacers over the boxed diamonds?" help="We recommend to use this option only for experimental analysis of the data"/> <param argument="-f" truevalue="-f" falsevalue="" type="boolean" label="Skip the verification of the fasta file generated from the GFF file?" help="The verification is mainly based on the length of the spacer sequences. If a spacer is 1.5 time shorter or longer than the average spacer size of the dataset, a warning is raised and the script stops (Verification is ran by default)."/> <param name="cut_off" type="integer" optional="true" label="Score cutoff for pairing of the spacers"/> <param argument="-gU" truevalue="-gU" falsevalue="" type="boolean" label="Gray out unique?" help="The unique spacers will be grayed"/> <param argument="-gS" truevalue="-gS" falsevalue="" type="boolean" label="Gray out similar?" help="The conserved spacers will be grayed"/> <conditional name="rerun"> <param argument="-r" type="select" label="Change spacer colour?" help="Use this option to keep the same color attributed to the spacer during a previous analysis"> <option value="">No</option> <option value="-r">Yes</option> </param> <when value="-r"> <param name="prev_final" format="tabular" label="Previous spacer.mcl.final" type="data" help="Input a previous .final file you want to retain the colour from"/> <param name="prev_svg" format="svg" label="Previous SVG" type="data" help="Input a previous .svg file you want to retain the colour from"/> </when> <when value=""> </when> </conditional> <param name="outputs" type="select" multiple="true" display="checkboxes" label="Additional outputs"> <option value="out_fasta36">Fasta36</option> <option value="out_spacermatch">Spacermatch</option> <option value="out_spacermatch_mcl">Spacermatch MCL</option> <option value="out_spacermatch_mcl_col">Spacermatch MCL Col</option> </param> </inputs> <outputs> <data name="output_fasta" format="tabular" label="${tool.name} on ${on_string}: fasta output" from_work_dir="infile.fasta"/> <data name="output_fasta36" format="tabular" label="${tool.name} on ${on_string}: fasta_fast36 output" from_work_dir="infile.fasta_fasta36"> <filter>outputs and 'out_fasta36' in outputs</filter> </data> <data name="output_spacermatch" format="tabular" label="${tool.name} on ${on_string}: spacermatch output" from_work_dir="infile.fasta_fasta36.spacermatch"> <filter>outputs and 'out_spacermatch' in outputs</filter> </data> <data name="output_spacermatch_mcl" format="tabular" label="${tool.name} on ${on_string}: spacermatch.mcl output" from_work_dir="infile.fasta_fasta36.spacermatch.mcl"> <filter>outputs and 'out_spacermatch_mcl' in outputs</filter> </data> <data name="output_spacermatch_mcl_col" format="tabular" label="${tool.name} on ${on_string}: spacermatch.mcl.col output" from_work_dir="infile.fasta_fasta36.spacermatch.mcl.col"> <filter>outputs and 'out_spacermatch_mcl_col' in outputs</filter> </data> <data name="output_spacermatch_mcl_final" format="tabular" label="${tool.name} on ${on_string}: spacematch.mcl.final output" from_work_dir="infile.fasta_fasta36.spacermatch.mcl.final"/> <data name="output_svg" format="svg" label="${tool.name} on ${on_string}: SVG output" from_work_dir="infile.fasta_fasta36.spacermatch.mcl.svg"/> </outputs> <tests> <test expect_num_outputs="7"> <param name="input_data" value="crispr_test.gff" ftype="gff"/> <param name="outputs" value="out_fasta36,out_spacermatch,out_spacermatch_mcl_col,out_spacermatch_mcl"/> <output name="output_fasta" file="crispr_test.gff.fasta"/> <output name="output_fasta36"> <assert_contents> <has_text text="NC_010473"/> </assert_contents> </output> <output name="output_spacermatch" file="crispr_test.gff.fasta_fasta36.spacermatch"/> <output name="output_spacermatch_mcl" file="crispr_test.gff.fasta_fasta36.spacermatch.mcl"/> <output name="output_spacermatch_mcl_col"> <assert_contents> <has_text text="NC_010473"/> </assert_contents> </output> <output name="output_spacermatch_mcl_final"> <assert_contents> <has_text text="NC_010473"/> </assert_contents> </output> <output name="output_svg"> <assert_contents> <has_text text="svg"/> </assert_contents> </output> </test> <test expect_num_outputs="3"> <param name="input_data" value="crispr_test_adv.gff" ftype="gff"/> <param name="isolate_list" value="test_isolates.txt" ftype="txt"/> <param name="n" value="true"/> <output name="output_fasta" file="crispr_test_adv.gff.fasta"/> <output name="output_spacermatch_mcl_final"> <assert_contents> <has_text text="NC_010473"/> </assert_contents> </output> <output name="output_svg"> <assert_contents> <has_text text="svg"/> </assert_contents> </output> </test> </tests> <help><![CDATA[ **What it does** CRISPRStudio is a program developed to facilitate and accelerate CRISPR array visualization. It works by first comparing spacers sequence homology in a dataset, then assigning a two-color-code to each cluster of spacers and finally writing an svg file, which can be opened in graphics vector editor. ]]> </help> <citations> <citation type="bibtex"> @UNPUBLISHED{moineaulab2018, author = {moineaulab}, title = {CRISPRStudio: Program developed to facilitate and accelerate CRISPR array visualization}, year = {2018}, url = {https://github.com/moineaulab/CRISPRStudio}, } </citation> </citations> </tool>