Mercurial > repos > iuc > pretext_map

changeset 1:02831bf9e95f draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit 663ac3c3df3458f3bd5f1c9d49b3ebf9cd97f52c"
author iuc
date Thu, 20 May 2021 07:57:57 +0000
parents 7c2e9bc2123b
children 8fef980d48b5
files pretext_map.xml test-data/output_2.pretext test-data/test.sam
diffstat 3 files changed, 9 insertions(+), 4 deletions(-) [+]
line wrap: on
line diff
--- a/pretext_map.xml	Wed May 05 15:09:54 2021 +0000
+++ b/pretext_map.xml	Thu May 20 07:57:57 2021 +0000
@@ -1,6 +1,6 @@
 <tool id="pretext_map" name="PretextMap" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
     <macros>
-        <token name="@TOOL_VERSION@">0.1.5</token>
+        <token name="@TOOL_VERSION@">0.1.6</token>
         <token name="@VERSION_SUFFIX@">0</token>
     </macros>
     <requirements>
@@ -63,19 +63,21 @@
             </param>
             <when value=""/>
             <when value="in">
-                <param name="filter_list" type="text" label="Filter list" help="Comma separated list of sequence names to use as a filter" value="seq_1, seq_2">
+                <param name="filter_list" type="text" label="Filter list" help="Comma separated list of sequence names to use as a filter" value="seq_1,seq_2">
                     <sanitizer>
                         <valid initial="string.ascii_letters,string.digits">
                             <add value="_"/>
+                            <add value=","/>
                         </valid>
                     </sanitizer>
                 </param>
             </when>
             <when value="out">
-                <param name="filter_list" type="text" label="Filter list" help="Comma separated list of sequence names to use as a filter" value="seq_1, seq_2">
+                <param name="filter_list" type="text" label="Filter list" help="Comma separated list of sequence names to use as a filter" value="seq_1,seq_2">
                     <sanitizer>
                         <valid initial="string.ascii_letters,string.digits">
                             <add value="_"/>
+                            <add value=","/>
                         </valid>
                     </sanitizer>
                 </param>
@@ -107,7 +109,7 @@
             </conditional>
             <conditional name="filter">
                 <param name="filter_type" value="out"/>
-                <param name="filter_list" value="chrM, chr8, chr9"/>
+                <param name="filter_list" value="chrM,chr8,chr9"/>
             </conditional>
             <output name="pretext_map_out" file="output_2.pretext"/>
         </test>
Binary file test-data/output_2.pretext has changed
--- a/test-data/test.sam	Wed May 05 15:09:54 2021 +0000
+++ b/test-data/test.sam	Thu May 20 07:57:57 2021 +0000
@@ -1,3 +1,6 @@
+@HD	VN:1.3	SO:queryname
+@SQ	SN:ref	LN:45
+@SQ	SN:ref2	LN:40
 HWI-EAS269B:8:34:797:623	145	chr1	16632182	255	27M	=	16631977	0	CCATTTCCTGTATGCTGTAAAGTACAA	IIIIIIIIIIIIIIIIIIIIIIIIIII	NM:i:0	NH:i:1
 HWI-EAS269B:8:40:39:1184	145	chr1	24620331	3	27M	=	24620115	0	ATTTATGTGGTTTCGTTTACCTTCTAT	IIIIIIIIIIIIIIIIIIIIIIIIIII	NM:i:0	NH:i:2	CC:Z:chrM	CP:i:9060
 HWI-EAS269B:8:58:533:1198	81	chr1	88426079	255	27M	=	88423429	0	GAAGAGGAAGAAGGTGGGGAGGAAGAG	IIIG?IIIIIIIIIIIIIIIIIIIIII	NM:i:0	NH:i:1