diff lasttrain.xml @ 4:8705e0d74a0f draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 6b601baaf89634bc8d110ea06e3e64c7a585f3ba"

--- a/lasttrain.xml	Fri Nov 13 09:05:49 2020 +0000
+++ b/lasttrain.xml	Wed Mar 24 22:36:50 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="last_train" name="LAST-train" version="@LAST_CONDA_VERSION@+galaxy2" profile="18.01">
+<tool id="last_train" name="LAST-train" version="@LAST_CONDA_VERSION@+galaxy0" profile="20.01">
 
     <description>finds the rates (probabilities) of insertion, deletion, and substitutions between two sets of sequences.</description>
 
@@ -11,11 +11,16 @@
     </requirements>
 
     <command detect_errors="exit_code"><![CDATA[
+        set -e -o pipefail; 
         #if $db_opts.db_opts_input == 'lastdb'
             ln -s '$db_opts.lastdatabase.extra_files_path' './db_files' &&
         #end if
-
-        last-train
+        #if $query_fasta.ext.endswith('.gz')
+        zcat 
+        #else
+        cat 
+        #end if
+        '$query_fasta' | last-train
 
         -Q $init_options.Q
         -r $init_options.r
@@ -43,15 +48,13 @@
             'db_files/lastdb'
         #end if
 
-        '$query_fasta'
-
         >'$outfile'
 
     ]]></command>
 
     <inputs>
         <expand macro="input_db" />
-        <param name="query_fasta" type="data" format="fasta,fastqsanger" label="Queries input files" />
+        <param name="query_fasta" type="data" format="fasta,fasta.gz,fastqsanger,fastqsanger.gz" label="Queries input files" />
         <conditional name="init_options">            
             <param argument="-Q" type="select" multiple="false" label="Query input format">
                 <option value="0" selected="true">FASTA</option>
@@ -115,15 +118,15 @@
                     <param name="E" value="10"/>
                 </section>
             </section>
-            <param name="query_fasta" value="fuguMito.fa"/>
-            <output name="outfile" file="last_train_E.txt" ftype="txt" lines_diff="22"/>
+            <param name="query_fasta" value="fuguMito.fa.gz" ftype="fasta.gz"/>
+            <output name="outfile" file="last_train_E.txt" ftype="txt" lines_diff="28"/>
         </test>
         <test>
             <conditional name="db_opts">
                 <param name="db_opts_input" value="db"/>
                 <param name="database" value="humdb"/>
             </conditional>
-            <param name="query_fasta" value="fuguMito.fa"/>
+            <param name="query_fasta" value="fuguMito.fq.gz" ftype="fastqsanger.gz"/>
             <output name="outfile" file="last_train.txt" ftype="txt" lines_diff="22"/>
         </test>
     </tests>