Mercurial > repos > yating-l > ucsc_blat

changeset 13:820f68ad34a7 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_blat/ commit f38778f3a25020809c3f6cf17aafb8dbfc54b2e8
author iuc
date Sat, 28 Sep 2024 16:29:35 +0000
parents e79965d0351c
children
files blat.xml
diffstat 1 files changed, 35 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/blat.xml	Sat Dec 03 10:38:40 2022 +0000
+++ b/blat.xml	Sat Sep 28 16:29:35 2024 +0000
@@ -1,8 +1,8 @@
 <tool id="ucsc_blat" name="UCSC BLAT Alignment Tool" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
     <description>BLAST-like sequence alignment tool</description>
     <macros>
-        <token name="@TOOL_VERSION@">377</token>
-        <token name="@VERSION_SUFFIX@">1</token>
+        <token name="@TOOL_VERSION@">469</token>
+        <token name="@VERSION_SUFFIX@">0</token>
 
         <xml name="mask_cond" tokens="maskarg,label,help">
             <conditional name="@MASKARG@_type">
@@ -180,6 +180,8 @@
         <param name="out" type="select" label="Select output file format (-out)">
             <option value="psl">Tab-separated format, no sequence (psl)</option>
             <option value="psl -noHead">Tab-separated format, no sequence, no header (psl -noHead)</option>
+            <option value="pslx">Tab-separated format (pslx)</option>
+            <option value="pslx -noHead">Tab-separated format, no header (pslx -noHead)</option>
             <option value="axt">Blastz-associated axt format (axt)</option>
             <option value="maf">Multiz-associated maf format (maf)</option>
             <option value="sim4">Similar to sim4 format (sim4)</option>
@@ -238,7 +240,37 @@
                 <param name="stepSize" value="5"/><!--explicitly set default .. to check if it is on the CL-->
             </section>
             <param name="out" value="psl -noHead" />
-            <output name="output" value="dbia3/dbia3.sorted.psl" ftype="tabular" sort="true"/>
+            <output name="output" value="dbia3/dbia3.sorted.psl" ftype="tabular" sort="true">
+                <assert_contents>
+                    <has_n_columns n="21"/>
+                </assert_contents>
+            </output>
+            <assert_command>
+                <has_text text="-tileSize=5"/>
+                <has_text text="-mask" negate="true"/>
+            </assert_command>
+        </test>
+        <test>
+            <conditional name="reference_source">
+                <param name="reference_source_selector" value="cached"/>
+                <param name="database" value="dbdia display name"/>
+            </conditional>
+            <param name="query" value="dbia3/dmel-transcript.fa" ftype="fasta" />
+            <param name="database_type" value="dnax" />
+            <param name="query_type" value="rnax" />
+            <section name="basic_align">
+                <param name="maxIntron" value="" />
+            </section>
+            <section name="adv_align">
+                <param name="tileSize" value="5"/><!--explicitly set default .. to check if it is on the CL-->
+                <param name="stepSize" value="5"/><!--explicitly set default .. to check if it is on the CL-->
+            </section>
+            <param name="out" value="pslx -noHead" />
+            <output name="output" value="dbia3/dbia3.sorted.psl" ftype="tabular" sort="true" compare="contains">
+                <assert_contents>
+                    <has_n_columns n="23"/>
+                </assert_contents>
+            </output>
             <assert_command>
                 <has_text text="-tileSize=5"/>
                 <has_text text="-mask" negate="true"/>