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changeset 1:86206f93fb13 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 67b8e5adffa4015ee60b1b4a0cd220f632ba1082"
author iuc
date Wed, 22 Jul 2020 19:50:13 -0400
parents 9a7e91fc6562
children bf30030e5265
files lastal.xml lastdb.xml lasttrain.xml tool_data_table_conf.xml
diffstat 4 files changed, 17 insertions(+), 12 deletions(-) [+]
line wrap: on
line diff
--- a/lastal.xml	Wed Jun 17 14:50:21 2020 -0400
+++ b/lastal.xml	Wed Jul 22 19:50:13 2020 -0400
@@ -1,4 +1,4 @@
-<tool id="last_al" name="LASTal" version="@LAST_CONDA_VERSION@+galaxy0" profile="18.01">
+<tool id="last_al" name="LASTal" version="@LAST_CONDA_VERSION@+galaxy1" profile="18.01">
 
     <description>finds local alignments between query sequences, and reference sequences.</description>
 
@@ -75,15 +75,14 @@
 
     <inputs>
         <expand macro="input_db"/>
-        <param name="query_fasta" type="data" format="FASTA" label="Queries fasta file"/>
+        <param name="query_fasta" type="data" format="fasta,fastqsanger,fastqsolexa,fastqillumina,tabular" label="Queries FASTA file"/>
 
         <section name="lastal" title="Lastal arguments" expanded="true">
-            <param argument="-Q" type="select" multiple="false" label="Input format">
-                <option value="0" selected="true">fasta or fastq-ignore</option>
+            <param argument="-Q" type="select" multiple="false" label="Query input format">
+                <option value="0" selected="true">FASTA</option>
                 <option value="1">fastq-sanger</option>
                 <option value="2">fastq-solexa</option>
                 <option value="3">fastq-illumina</option>
-                <option value="4">prb</option>
                 <option value="5">PSSM</option>
             </param>            
             <param argument="-f" type="select" multiple="false" label="Output format">
--- a/lastdb.xml	Wed Jun 17 14:50:21 2020 -0400
+++ b/lastdb.xml	Wed Jul 22 19:50:13 2020 -0400
@@ -1,4 +1,4 @@
-<tool id="last_db" name="LASTdb" version="@LAST_CONDA_VERSION@+galaxy0" profile="18.01">
+<tool id="last_db" name="LASTdb" version="@LAST_CONDA_VERSION@+galaxy1" profile="18.01">
 
     <description>prepares sequences for subsequent comparison and alignment using lastal.</description>
 
@@ -36,10 +36,10 @@
     ]]></command>
 
     <inputs>
-        <param name="input_files" type="data" format="FASTA" label="Reference(s) input files" />
+        <param name="input_files" type="data" format="fasta,fastqsanger,fastqsolexa,fastqillumina" label="Reference(s) input files" />
         <section name="lastdb" title="Lastdb arguments" expanded="true">
             <param argument="-Q" type="select" multiple="false" label="Input format">
-                <option value="0" selected="true">fasta or fastq-ignore</option>
+                <option value="0" selected="true">FASTA</option>
                 <option value="1">fastq-sanger</option>
                 <option value="2">fastq-solexa</option>
                 <option value="3">fastq-illumina</option>
--- a/lasttrain.xml	Wed Jun 17 14:50:21 2020 -0400
+++ b/lasttrain.xml	Wed Jul 22 19:50:13 2020 -0400
@@ -1,4 +1,4 @@
-<tool id="last_train" name="LAST-train" version="@LAST_CONDA_VERSION@+galaxy0" profile="18.01">
+<tool id="last_train" name="LAST-train" version="@LAST_CONDA_VERSION@+galaxy1" profile="18.01">
 
     <description>finds the rates (probabilities) of insertion, deletion, and substitutions between two sets of sequences.</description>
 
@@ -52,10 +52,10 @@
 
     <inputs>
         <expand macro="input_db" />
-        <param name="query_fasta" type="data" format="FASTA" label="Queries input files" />
+        <param name="query_fasta" type="data" format="fasta,fastqsanger" label="Queries input files" />
         <conditional name="init_options">            
-            <param argument="-Q" type="select" multiple="false" label="Input format">
-                <option value="0" selected="true">Fasta or fastq-ignore</option>
+            <param argument="-Q" type="select" multiple="false" label="Query input format">
+                <option value="0" selected="true">FASTA</option>
                 <option value="1">Fastq-sanger</option>
             </param>
             <when value="0">
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml	Wed Jul 22 19:50:13 2020 -0400
@@ -0,0 +1,6 @@
+<tables>
+    <table name="lastdb" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="test-data/lastdb.loc" />
+    </table>
+</tables>