Mercurial > repos > richard-burhans > rdeval
changeset 6:24b05d3958d7 draft
planemo upload for repository https://github.com/vgl-hub/rdeval commit 344add351131179b6c41777e7574823ef678e7a7
author | richard-burhans |
---|---|
date | Mon, 05 May 2025 17:51:10 +0000 |
parents | 7cfeba6facd1 |
children | 40a03830a38c |
files | macros.xml rdeval.xml static/images/pipeline.svg |
diffstat | 3 files changed, 27 insertions(+), 19 deletions(-) [+] |
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--- a/macros.xml Fri May 02 22:49:30 2025 +0000 +++ b/macros.xml Mon May 05 17:51:10 2025 +0000 @@ -5,7 +5,7 @@ </requirements> </xml> <token name="@TOOL_VERSION@">0.0.7</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> <token name="@PROFILE@">23.02</token> <xml name="citations"> <citations>
--- a/rdeval.xml Fri May 02 22:49:30 2025 +0000 +++ b/rdeval.xml Mon May 05 17:51:10 2025 +0000 @@ -9,7 +9,12 @@ #set $mangled_inputs = [] #for $input in $input_reads #set $mangled_base = re.sub(r"[^\w\-\s]", "_", str($input.element_identifier)) - #set $mangled_input = $mangled_base + "." + str($input.ext) + #if str($input.ext).lower().startswith("fastq") + #set $mangled_ext = "fastq" + #else + #set $mangled_ext = str($input.ext) + #end if + #set $mangled_input = $mangled_base + "." + $mangled_ext #silent $mangled_inputs.append($mangled_input) ln -s '$input' '$mangled_input' && #end for @@ -82,7 +87,7 @@ <param argument="--include-list" type="data" format="txt" optional="true" label="File containing headers to include"/> <param argument="--exclude-list" type="data" format="txt" optional="true" label="File containing headers to exclude"/> <conditional name="filter_expression"> - <param name="filter_selector" type="select" label="Filter using length and/or quality" help="filter help"> + <param name="filter_selector" type="select" label="Filter using length and/or quality" help="Retain reads matching filter"> <option value="no_exp" selected="true">No</option> <option value="l_exp">Read length</option> <option value="q_exp">Average read quality</option> @@ -268,6 +273,8 @@ **rdeval** accepts an arbitrary number of sequencing files and optionally **filters**, **subsamples**, and/or **compresses homopolymers** within the reads. The retained reads can be saved in multiple formats, and metrics on these reads can be stored in a '*sketch*' file. Statistics can then be efficiently retrieved from these sketch files for further processing. .. image:: pipeline.svg + :alt: pipeline diagram + :align: left Filtering =========
--- a/static/images/pipeline.svg Fri May 02 22:49:30 2025 +0000 +++ b/static/images/pipeline.svg Mon May 05 17:51:10 2025 +0000 @@ -2,9 +2,9 @@ <!-- Created with Inkscape (http://www.inkscape.org/) --> <svg - width="210mm" - height="297mm" - viewBox="0 0 210 297" + width="107.91907mm" + height="176.97755mm" + viewBox="0 0 107.91907 176.97755" version="1.1" id="svg5" xmlns="http://www.w3.org/2000/svg" @@ -12,27 +12,27 @@ <defs id="defs2"> <marker - style="overflow:visible;" + style="overflow:visible" id="marker1298" - refX="0.0" - refY="0.0" + refX="0" + refY="0" orient="auto"> <path - transform="scale(0.8) rotate(180) translate(12.5,0)" - style="fill-rule:evenodd;fill:context-stroke;stroke:context-stroke;stroke-width:1.0pt;" - d="M 0.0,0.0 L 5.0,-5.0 L -12.5,0.0 L 5.0,5.0 L 0.0,0.0 z " + transform="matrix(-0.8,0,0,-0.8,-10,0)" + style="fill:context-stroke;fill-rule:evenodd;stroke:context-stroke;stroke-width:1pt" + d="M 0,0 5,-5 -12.5,0 5,5 Z" id="path892" /> </marker> <marker - style="overflow:visible;" + style="overflow:visible" id="Arrow1Lend" - refX="0.0" - refY="0.0" + refX="0" + refY="0" orient="auto"> <path - transform="scale(0.8) rotate(180) translate(12.5,0)" - style="fill-rule:evenodd;fill:context-stroke;stroke:context-stroke;stroke-width:1.0pt;" - d="M 0.0,0.0 L 5.0,-5.0 L -12.5,0.0 L 5.0,5.0 L 0.0,0.0 z " + transform="matrix(-0.8,0,0,-0.8,-10,0)" + style="fill:context-stroke;fill-rule:evenodd;stroke:context-stroke;stroke-width:1pt" + d="M 0,0 5,-5 -12.5,0 5,5 Z" id="path36356" /> </marker> <marker @@ -133,7 +133,8 @@ </marker> </defs> <g - id="layer1"> + id="layer1" + transform="translate(-16.361184,-35.29722)"> <g id="g4714"> <g