Mercurial > repos > iuc > ucsc_fasplit

changeset 3:d3f58a0dc09d draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fasplit commit 303002db06287fb25306020c4391626842f52162
author iuc
date Sun, 22 Sep 2024 07:26:24 +0000
parents bf04bd405d5b
children
files fasplit.xml
diffstat 1 files changed, 34 insertions(+), 30 deletions(-) [+]
line wrap: on
line diff
--- a/fasplit.xml	Wed Feb 02 13:56:02 2022 +0000
+++ b/fasplit.xml	Sun Sep 22 07:26:24 2024 +0000
@@ -1,11 +1,11 @@
-<tool id="fasplit" name="faSplit" version="@TOOL_VERSION@">
+<tool id="fasplit" name="faSplit" version="@TOOL_VERSION@" profile="22.05">
     <description>Split a FASTA file</description>
+    <macros>
+        <token name="@TOOL_VERSION@">469</token>
+    </macros>
     <xrefs>
         <xref type="bio.tools">UCSC_Genome_Browser_Utilities</xref>
     </xrefs>
-    <macros>
-        <token name="@TOOL_VERSION@">377</token>
-    </macros>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">ucsc-fasplit</requirement>
     </requirements>
@@ -57,52 +57,52 @@
                 <element name="2" file="2.fa" />
                 <element name="3" file="3.fa" />
                 <element name="4" file="4.fa" />
-            </output_collection>    
+            </output_collection>
         </test>
         <test>
             <param name="input" ftype="fasta" value="CDS.fa"/>
             <param name="split_type" value="byname"/>
             <output_collection name="output_list" type="list">
                 <element name="ENSCAFT00000022939_canisfamiliaris" file="ENSCAFT00000022939_canisfamiliaris.fa" />
+                <element name="ENSCAFT00000022963_canisfamiliaris" file="ENSCAFT00000022963_canisfamiliaris.fa" />
+                <element name="ENSCAFT00000025950_canisfamiliaris" file="ENSCAFT00000025950_canisfamiliaris.fa" />
+                <element name="ENSMUST00000026013_musmusculus" file="ENSMUST00000026013_musmusculus.fa" />
+                <element name="ENSMUST00000040820_musmusculus" file="ENSMUST00000040820_musmusculus.fa" />
+                <element name="ENSMUST00000041588_musmusculus" file="ENSMUST00000041588_musmusculus.fa" />
+                <element name="ENSMUST00000091291_musmusculus" file="ENSMUST00000091291_musmusculus.fa" />
+                <element name="ENSMUST00000100505_musmusculus" file="ENSMUST00000100505_musmusculus.fa" />
+                <element name="ENSMUST00000110806_musmusculus" file="ENSMUST00000110806_musmusculus.fa" />
+                <element name="ENSMUST00000153440_musmusculus" file="ENSMUST00000153440_musmusculus.fa" />
+                <element name="ENSMUST00000163344_musmusculus" file="ENSMUST00000163344_musmusculus.fa" />
+                <element name="ENSMUST00000168613_musmusculus" file="ENSMUST00000168613_musmusculus.fa" />
+                <element name="ENSMUST00000173143_musmusculus" file="ENSMUST00000173143_musmusculus.fa" />
                 <element name="ENSMUST00000207100_musmusculus" file="ENSMUST00000207100_musmusculus.fa" />
-                <element name="ENSSSCT00000014817_susscrofa" file="ENSSSCT00000014817_susscrofa.fa" />
-                <element name="ENSCAFT00000022963_canisfamiliaris" file="ENSCAFT00000022963_canisfamiliaris.fa" />
                 <element name="ENSMUST00000208839_musmusculus" file="ENSMUST00000208839_musmusculus.fa" />
-                <element name="ENSSSCT00000023183_susscrofa" file="ENSSSCT00000023183_susscrofa.fa" />
-                <element name="ENSCAFT00000025950_canisfamiliaris" file="ENSCAFT00000025950_canisfamiliaris.fa" />
                 <element name="ENSPTRT00000019089_pantroglodytes" file="ENSPTRT00000019089_pantroglodytes.fa" />
-                <element name="ENSSSCT00000032764_susscrofa" file="ENSSSCT00000032764_susscrofa.fa" />
-                <element name="ENSMUST00000026013_musmusculus" file="ENSMUST00000026013_musmusculus.fa" />
                 <element name="ENSPTRT00000034846_pantroglodytes" file="ENSPTRT00000034846_pantroglodytes.fa" />
+                <element name="ENSPTRT00000040520_pantroglodytes" file="ENSPTRT00000040520_pantroglodytes.fa" />
+                <element name="ENSPTRT00000040521_pantroglodytes" file="ENSPTRT00000040521_pantroglodytes.fa" />
+                <element name="ENSRNOT00000041155_rattusnorvegicus" file="ENSRNOT00000041155_rattusnorvegicus.fa" />
+                <element name="ENSRNOT00000044009_rattusnorvegicus" file="ENSRNOT00000044009_rattusnorvegicus.fa" />
+                <element name="ENSRNOT00000064726_rattusnorvegicus" file="ENSRNOT00000064726_rattusnorvegicus.fa" />
+                <element name="ENSRNOT00000066674_rattusnorvegicus" file="ENSRNOT00000066674_rattusnorvegicus.fa" />
+                <element name="ENSRNOT00000067448_rattusnorvegicus" file="ENSRNOT00000067448_rattusnorvegicus.fa" />
+                <element name="ENSSSCT00000008295_susscrofa" file="ENSSSCT00000008295_susscrofa.fa" />
+                <element name="ENSSSCT00000013404_susscrofa" file="ENSSSCT00000013404_susscrofa.fa" />
+                <element name="ENSSSCT00000014817_susscrofa" file="ENSSSCT00000014817_susscrofa.fa" />
+                <element name="ENSSSCT00000023183_susscrofa" file="ENSSSCT00000023183_susscrofa.fa" />
+                <element name="ENSSSCT00000032764_susscrofa" file="ENSSSCT00000032764_susscrofa.fa" />
                 <element name="ENSSSCT00000033745_susscrofa" file="ENSSSCT00000033745_susscrofa.fa" />
-                <element name="ENSMUST00000040820_musmusculus" file="ENSMUST00000040820_musmusculus.fa" />
-                <element name="ENSPTRT00000040520_pantroglodytes" file="ENSPTRT00000040520_pantroglodytes.fa" />
                 <element name="ENSSSCT00000035258_susscrofa" file="ENSSSCT00000035258_susscrofa.fa" />
-                <element name="ENSMUST00000041588_musmusculus" file="ENSMUST00000041588_musmusculus.fa" />
-                <element name="ENSPTRT00000040521_pantroglodytes" file="ENSPTRT00000040521_pantroglodytes.fa" />
                 <element name="ENST00000302850_homosapiens" file="ENST00000302850_homosapiens.fa" />
-                <element name="ENSMUST00000091291_musmusculus" file="ENSMUST00000091291_musmusculus.fa" />
-                <element name="ENSRNOT00000041155_rattusnorvegicus" file="ENSRNOT00000041155_rattusnorvegicus.fa" />
                 <element name="ENST00000338702_homosapiens" file="ENST00000338702_homosapiens.fa" />
-                <element name="ENSMUST00000100505_musmusculus" file="ENSMUST00000100505_musmusculus.fa" />
-                <element name="ENSRNOT00000044009_rattusnorvegicus" file="ENSRNOT00000044009_rattusnorvegicus.fa" />
                 <element name="ENST00000340611_homosapiens" file="ENST00000340611_homosapiens.fa" />
-                <element name="ENSMUST00000110806_musmusculus" file="ENSMUST00000110806_musmusculus.fa" />
-                <element name="ENSRNOT00000064726_rattusnorvegicus" file="ENSRNOT00000064726_rattusnorvegicus.fa" />
                 <element name="ENST00000341500_homosapiens" file="ENST00000341500_homosapiens.fa" />
-                <element name="ENSMUST00000153440_musmusculus" file="ENSMUST00000153440_musmusculus.fa" />
-                <element name="ENSRNOT00000066674_rattusnorvegicus" file="ENSRNOT00000066674_rattusnorvegicus.fa" />
                 <element name="ENST00000378069_homosapiens" file="ENST00000378069_homosapiens.fa" />
-                <element name="ENSMUST00000163344_musmusculus" file="ENSMUST00000163344_musmusculus.fa" />
-                <element name="ENSRNOT00000067448_rattusnorvegicus" file="ENSRNOT00000067448_rattusnorvegicus.fa" />
                 <element name="ENST00000421712_homosapiens" file="ENST00000421712_homosapiens.fa" />
-                <element name="ENSMUST00000168613_musmusculus" file="ENSMUST00000168613_musmusculus.fa" />
-                <element name="ENSSSCT00000008295_susscrofa" file="ENSSSCT00000008295_susscrofa.fa" />
                 <element name="ENST00000542639_homosapiens" file="ENST00000542639_homosapiens.fa" />
-                <element name="ENSMUST00000173143_musmusculus" file="ENSMUST00000173143_musmusculus.fa" />
-                <element name="ENSSSCT00000013404_susscrofa" file="ENSSSCT00000013404_susscrofa.fa" />
                 <element name="ENST00000600492_homosapiens" file="ENST00000600492_homosapiens.fa" />
-            </output_collection>    
+            </output_collection>
         </test>
     </tests>
     <help><![CDATA[
@@ -110,8 +110,12 @@
 
 `faSplit`_ is a tool to split a single FASTA file into several files.
 
+For implementation details see faSplit's `source code`_.
+
 .. _faSplit: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/FOOTER.txt
+.. _source code: https://github.com/ucscGenomeBrowser/kent/blob/master/src/utils/faSplit/faSplit.c
     ]]></help>
     <citations>
+        <citation type="doi">10.1093/bib/bbs038</citation>
     </citations>
 </tool>