diff lastdb.xml @ 2:bf30030e5265 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit d48fa8fc8724e2a1c659dde00cad9d6db3e710db"

--- a/lastdb.xml	Wed Jul 22 19:50:13 2020 -0400
+++ b/lastdb.xml	Thu Sep 10 16:08:15 2020 +0000
@@ -11,8 +11,17 @@
     </requirements>
 
     <command detect_errors="exit_code"><![CDATA[
-        lastdb 
-        -Q $lastdb.Q
+        lastdb
+
+        #if $input_files.ext == 'fasta'
+            -Q 0
+        #else if $input_files.ext == 'fastqsanger'
+            -Q 1
+        #else if $input_files.ext == 'fastqsolexa'
+            -Q 2
+        #else if $input_files.ext == 'fastqillumina'
+            -Q 3
+        #end if
         $lastdb.sequences_type.protein 
         -a $lastdb.sequences_type.a
         -R $lastdb.repeats.uppercase$lastdb.repeats.simple_repeat 
@@ -32,19 +41,12 @@
         &&
 
         mkdir '$outfile.files_path' &&
-        mv lastdb.* '$outfile.files_path'
+        mv lastdb* '$outfile.files_path'
     ]]></command>
 
     <inputs>
         <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</option>
-                <option value="1">fastq-sanger</option>
-                <option value="2">fastq-solexa</option>
-                <option value="3">fastq-illumina</option>
-            </param>
-
             <conditional name="sequences_type">
                 <param name="protein" type="select" multiple="false" label="The sequences are :">
                     <option value="" selected="true">DNA</option>
@@ -167,6 +169,26 @@
                 <extra_files type="file" value="hedgdb.tis" name="lastdb.tis" compare="sim_size" delta="1"/>
             </output>
         </test>
+        <test>
+            <param name="input_files" value="humanMito.fq" ftype="fastqsanger"/>
+            <section name="lastdb">
+                <param name="Q" value="1"/>
+                <section name="repeats">
+                    <param name="uppercase" value="0"/>
+                    <param name="simple_repeat" value="1"/>
+                    <param name="sm_lower" value="true"/>
+                </section>
+            </section>
+            <output name="outfile" compare="contains" file="hedgdb.lastdb" ftype="lastdb">
+                <extra_files type="file" value="humdb-sanger.bck" name="lastdb.bck" compare="sim_size" delta="1"/>
+                <extra_files type="file" value="humdb-sanger.des" name="lastdb.des"/>
+                <extra_files type="file" value="humdb-sanger.prj" name="lastdb.prj" lines_diff="1"/>
+                <extra_files type="file" value="humdb-sanger.sds" name="lastdb.sds"/>
+                <extra_files type="file" value="humdb-sanger.ssp" name="lastdb.ssp" compare="sim_size" delta="1"/>
+                <extra_files type="file" value="humdb-sanger.suf" name="lastdb.suf" compare="sim_size" delta="1"/>
+                <extra_files type="file" value="humdb-sanger.tis" name="lastdb.tis" compare="sim_size" delta="1"/>
+            </output>
+        </test>
     </tests>
 
     <help>@LAST_HELP@</help>