Mercurial > repos > iuc > seqtk

changeset 2:f73729b62b51 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 2249d643284ee782d882cd200729a86a2c6bb744
author iuc
date Fri, 01 Jan 2016 14:49:42 -0500
parents 61718851f199
children bc7d99f46a5d
files macros.xml seqtk_comp.xml seqtk_cutN.xml seqtk_dropse.xml seqtk_fqchk.xml seqtk_hety.xml seqtk_listhet.xml seqtk_mergefa.xml seqtk_mergepe.xml seqtk_mutfa.xml seqtk_randbase.xml seqtk_sample.xml seqtk_seq.xml seqtk_subseq.xml seqtk_trimfq.xml
diffstat 15 files changed, 24 insertions(+), 5 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Thu Feb 05 12:00:43 2015 -0500
+++ b/macros.xml	Fri Jan 01 14:49:42 2016 -0500
@@ -30,4 +30,8 @@
 <https://github.com/lh3/seqtk/>`_, developed by Heng Li at the Broad Institute
   ]]>
   </token>
+  <xml name="citation">
+      <citations>
+      </citations>
+  </xml>
 </macros>
--- a/seqtk_comp.xml	Thu Feb 05 12:00:43 2015 -0500
+++ b/seqtk_comp.xml	Fri Jan 01 14:49:42 2016 -0500
@@ -49,4 +49,5 @@
 
 @ATTRIBUTION@
 ]]></help>
+  <expand macro="citation" />
 </tool>
--- a/seqtk_cutN.xml	Thu Feb 05 12:00:43 2015 -0500
+++ b/seqtk_cutN.xml	Fri Jan 01 14:49:42 2016 -0500
@@ -48,5 +48,6 @@
 
 
 @ATTRIBUTION@
-      ]]></help>
+]]></help>
+  <expand macro="citation" />
 </tool>
--- a/seqtk_dropse.xml	Thu Feb 05 12:00:43 2015 -0500
+++ b/seqtk_dropse.xml	Fri Jan 01 14:49:42 2016 -0500
@@ -72,5 +72,6 @@
 
 
 @ATTRIBUTION@
-      ]]></help>
+]]></help>
+  <expand macro="citation" />
 </tool>
--- a/seqtk_fqchk.xml	Thu Feb 05 12:00:43 2015 -0500
+++ b/seqtk_fqchk.xml	Fri Jan 01 14:49:42 2016 -0500
@@ -55,4 +55,5 @@
 
 @ATTRIBUTION@
 ]]></help>
+  <expand macro="citation" />
 </tool>
--- a/seqtk_hety.xml	Thu Feb 05 12:00:43 2015 -0500
+++ b/seqtk_hety.xml	Fri Jan 01 14:49:42 2016 -0500
@@ -70,4 +70,5 @@
 
 @ATTRIBUTION@
 ]]></help>
+  <expand macro="citation" />
 </tool>
--- a/seqtk_listhet.xml	Thu Feb 05 12:00:43 2015 -0500
+++ b/seqtk_listhet.xml	Fri Jan 01 14:49:42 2016 -0500
@@ -44,4 +44,5 @@
 
 @ATTRIBUTION@
 ]]></help>
+  <expand macro="citation" />
 </tool>
--- a/seqtk_mergefa.xml	Thu Feb 05 12:00:43 2015 -0500
+++ b/seqtk_mergefa.xml	Fri Jan 01 14:49:42 2016 -0500
@@ -65,4 +65,5 @@
 
 @ATTRIBUTION@
 ]]></help>
+  <expand macro="citation" />
 </tool>
--- a/seqtk_mergepe.xml	Thu Feb 05 12:00:43 2015 -0500
+++ b/seqtk_mergepe.xml	Fri Jan 01 14:49:42 2016 -0500
@@ -90,4 +90,5 @@
 
 @ATTRIBUTION@
 ]]></help>
+  <expand macro="citation" />
 </tool>
--- a/seqtk_mutfa.xml	Thu Feb 05 12:00:43 2015 -0500
+++ b/seqtk_mutfa.xml	Fri Jan 01 14:49:42 2016 -0500
@@ -48,4 +48,5 @@
 
 @ATTRIBUTION@
 ]]></help>
+  <expand macro="citation" />
 </tool>
--- a/seqtk_randbase.xml	Thu Feb 05 12:00:43 2015 -0500
+++ b/seqtk_randbase.xml	Fri Jan 01 14:49:42 2016 -0500
@@ -42,4 +42,5 @@
 
 @ATTRIBUTION@
 ]]></help>
+  <expand macro="citation" />
 </tool>
--- a/seqtk_sample.xml	Thu Feb 05 12:00:43 2015 -0500
+++ b/seqtk_sample.xml	Fri Jan 01 14:49:42 2016 -0500
@@ -13,7 +13,7 @@
   <inputs>
     <expand macro="in_faq" />
     <param label="RNG seed" help="(-s)" name="s" type="integer" value="4"/>
-    <param label="Subsample (decimal fraction or number)" name="subsample_size" type="integer" value="100"/>
+    <param label="Subsample (decimal fraction or number)" name="subsample_size" type="float" value="100"/>
   </inputs>
   <outputs>
     <data format_source="in_file" hidden="false" name="default" label="Subsample of reads from $in_file.name"/>
@@ -35,4 +35,5 @@
 
 @ATTRIBUTION@
 ]]></help>
+  <expand macro="citation" />
 </tool>
--- a/seqtk_seq.xml	Thu Feb 05 12:00:43 2015 -0500
+++ b/seqtk_seq.xml	Fri Jan 01 14:49:42 2016 -0500
@@ -26,7 +26,9 @@
 $N
 $x1
 $x2
-$V
+#if $in_file.ext == "fastqillumina"
+ -V
+#end if
 
 $in_file
 > $default]]></command>
@@ -48,7 +50,6 @@
     <param checked="false" label="drop sequences containing ambiguous bases" help="(-N)" name="N" type="boolean" falsevalue="" truevalue="-N"/>
     <param checked="false" label="output the 2n-1 reads only" help="(-1)" name="x1" type="boolean" falsevalue="" truevalue="-1"/>
     <param checked="false" label="output the 2n reads only" help="(-2)" name="x2" type="boolean" falsevalue="" truevalue="-2"/>
-    <param checked="false" label="shift quality by '(-Q) - 33' " help="(-V)" name="V" type="boolean" falsevalue="" truevalue="-V"/>
   </inputs>
   <outputs>
     <data format_source="in_file" hidden="false" name="default"/>
@@ -73,4 +74,5 @@
 
 @ATTRIBUTION@
 ]]></help>
+  <expand macro="citation" />
 </tool>
--- a/seqtk_subseq.xml	Thu Feb 05 12:00:43 2015 -0500
+++ b/seqtk_subseq.xml	Fri Jan 01 14:49:42 2016 -0500
@@ -80,4 +80,5 @@
 
 @ATTRIBUTION@
 ]]></help>
+  <expand macro="citation" />
 </tool>
--- a/seqtk_trimfq.xml	Thu Feb 05 12:00:43 2015 -0500
+++ b/seqtk_trimfq.xml	Fri Jan 01 14:49:42 2016 -0500
@@ -59,4 +59,5 @@
 
 @ATTRIBUTION@
 ]]></help>
+  <expand macro="citation" />
 </tool>