Mercurial > repos > iuc > seqkit_locate

changeset 1:6510652376b1 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit e0bd99c950e2c5f403474fad5af0be3829c93607
author iuc
date Sun, 06 Nov 2022 17:48:00 +0000
parents 642d73815dd1
children 13604b5e9d30
files macros.xml seqkit_locate.xml
diffstat 2 files changed, 20 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Thu Nov 03 19:35:37 2022 +0000
+++ b/macros.xml	Sun Nov 06 17:48:00 2022 +0000
@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">2.3.1</token>
-    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@VERSION_SUFFIX@">1</token>
     <token name="@PROFILE@">20.09</token>
     <xml name="bio_tools">
         <xrefs>
--- a/seqkit_locate.xml	Thu Nov 03 19:35:37 2022 +0000
+++ b/seqkit_locate.xml	Sun Nov 06 17:48:00 2022 +0000
@@ -32,6 +32,7 @@
 $advanced_options.non_greedy
 $advanced_options.only_positive_strand
 $advanced_options.id_ncbi
+--seq-type $seq_type
 '${input_identifier}'
 > '$output'
 ]]></command>
@@ -73,6 +74,12 @@
                 <param argument="--pattern-file" type="data" format="fasta" label="Pattern/motif file"/>
             </when>
         </conditional>
+        <param argument="--seq-type" type="select" label="Sequence type" help="For automatic detection, it automatically detect by the first sequence. Default: auto">
+            <option value="auto">Automatic detection</option>
+            <option value="dna">DNA</option>
+            <option value="rna">RNA</option>
+            <option value="protein">Protein</option>
+        </param>
         <param name="output_mode" type="select" label="Output mode">
             <option value="">Tabular (default format)</option>
             <option value="--gtf">GTF</option>
@@ -143,6 +150,18 @@
             </section>
             <output name="output" file="locate_output3.gtf" ftype="gtf"/>
         </test>
+        <test expect_num_outputs="1">
+            <param name="input" value="input1.fasta.gz" ftype="fasta.gz"/>
+            <conditional name="conditional_pattern">
+                <param name="mode" value="expression"/>
+                <param name="pattern" value="ATAGAT"/>
+            </conditional>
+            <param name="seq_type" value="dna"/>
+            <section name="advanced_options">
+                <param name="max_mismatch" value="1"/>
+            </section>
+            <output name="output" file="locate_output1.tabular" ftype="tabular"/>
+        </test>
     </tests>
     <help>
 .. class:: infomark