Mercurial > repos > iuc > fastqe

diff fastqe.xml @ 2:cbedff6218a3 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe commit 4edf8f17bc1a8aaf25622afc9c0c048ff7fa2f0f"
author iuc
date Fri, 24 Jul 2020 19:13:07 +0000
parents 01902d7aa584
children 82a8161b6a19
line wrap: on
line diff
--- a/fastqe.xml	Mon Jul 20 12:03:42 2020 +0000
+++ b/fastqe.xml	Fri Jul 24 19:13:07 2020 +0000
@@ -1,13 +1,17 @@
-<tool id="fastqe" name="FASTQE" version="0.2.6">
+<tool id="fastqe" name="FASTQE" version="0.2.6+galaxy0">
     <description>visualize fastq files with emoji's 🧬😎</description>
     <requirements>
         <requirement type="package" version="0.2.6">fastqe</requirement>
+        <requirement type="package" version="4.7">sed</requirement>
     </requirements>
     <command detect_errors="exit_code">
     <![CDATA[
 
-    #for i in $input:
-        ln -s '$i' '$i.element_identifier' &&
+    #import re
+
+    #set $filenames = [re.sub('[^\w\-\s.]', '_', $i.element_identifier) for $i in $input]
+    #for $i, $filename in zip($input, $filenames):
+        ln -s '$i' '$filename' &&
     #end for
 
     echo "<html><head><title>FASTQE Report 🤔</title></head><body><h1>FASTQE Report 🤔</h1>" > '$output' &&
@@ -18,8 +22,8 @@
         --min
         --long $long
         --max
-        #for i in $input:
-            '$i.element_identifier'
+        #for $filename in $filenames:
+            '$filename'
         #end for
         | sed 's/$/<br>/;s/^\([^\t]*\)\t\([^\t]*\)\t/<h2>\1: \2<\/h2>\n/' >> '$output' &&
 
@@ -52,8 +56,6 @@
 +=======+=======+
 | N     | 🚫    |
 +-------+-------+
-| N     | 🚫    |
-+-------+-------+
 | 2-9   | 💀    |
 +-------+-------+
 | 10–19 | 💩    |