Mercurial > repos > iuc > crispr_studio
diff crispr_studio.xml @ 0:7346619ad005 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crispr_studio/ commit d746438ee434696f2867394eca7a93d6ec704320"
| author | iuc |
|---|---|
| date | Wed, 14 Aug 2019 11:37:55 -0400 |
| parents | |
| children | a227c05e0a55 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/crispr_studio.xml Wed Aug 14 11:37:55 2019 -0400 @@ -0,0 +1,161 @@ +<?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> + <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 name="n" 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>