Mercurial > repos > richard-burhans > rdeval

changeset 6:24b05d3958d7 draft

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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(-) [+]
line wrap: on
line diff
--- 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