# HG changeset patch
# User dfornika
# Date 1569366687 14400
# Node ID aaec1fe5415f5f760ae15c026894e9ed13b21c86
# Parent  1a22c8de420504cd2c1df3ff673e0768e48adc9e
planemo upload for repository https://github.com/phac-nml/mob-suite commit 0dd60ac52b9d34ee1f446182eda78cb8c01de6d1-dirty

diff -r 1a22c8de4205 -r aaec1fe5415f mob_typer_zipped.xml
--- a/mob_typer_zipped.xml	Tue Sep 24 19:01:44 2019 -0400
+++ b/mob_typer_zipped.xml	Tue Sep 24 19:11:27 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="mob_typer" name="MOB-Typer" version="2.0.0">
+<tool id="mob_typer" name="MOB-Typer (zipped input)" version="2.0.0">
   <description>Get the plasmid type and mobility given its sequence</description>
   <requirements>
      <requirement type="package" version="2.0.0">mob_suite</requirement>
@@ -6,17 +6,19 @@
   <command detect_errors="exit_code">
   <![CDATA[
     tar -xzf "${input}" &&
-    mob_typer  --num_threads \${GALAXY_SLOTS:-4} --infile "${input.name}" 
-   --min_rep_evalue '$adv_param.min_rep_evalue_value'
-   --min_mob_evalue '$adv_param.min_mob_evalue_value'
-   --min_con_evalue '$adv_param.min_con_evalue_value'
-   --min_ori_evalue '$adv_param.min_ori_evalue_value'
-   --min_mpf_evalue '$adv_param.min_mpf_evalue'
-   --min_rep_ident '$adv_param.min_rep_ident'
-   --min_mob_ident '$adv_param.min_mob_ident'
-   --min_ori_ident '$adv_param.min_ori_ident'
-   --min_mpf_ident '$adv_param.min_mpf_ident'
-    --outdir '.';
+    for plasmid in plasmids/*.fasta; do
+      mob_typer  --num_threads \${GALAXY_SLOTS:-4} --infile $plasmid 
+        --min_rep_evalue '$adv_param.min_rep_evalue_value'
+        --min_mob_evalue '$adv_param.min_mob_evalue_value'
+        --min_con_evalue '$adv_param.min_con_evalue_value'
+        --min_ori_evalue '$adv_param.min_ori_evalue_value'
+        --min_mpf_evalue '$adv_param.min_mpf_evalue'
+        --min_rep_ident '$adv_param.min_rep_ident'
+        --min_mob_ident '$adv_param.min_mob_ident'
+        --min_ori_ident '$adv_param.min_ori_ident'
+        --min_mpf_ident '$adv_param.min_mpf_ident'
+        --outdir '.';
+    done
   ]]>
   </command>
   <inputs>
@@ -34,7 +36,7 @@
     </section>  
   </inputs>
   <outputs>
-    <data name="outfile1" label="${tool.name}: Plasmid report on ${input.name}" format="tabular">
+    <data name="mob_typer_report" label="${tool.name}: Plasmid report on ${input.name}" format="tabular">
       <discover_datasets pattern=".+_report\.txt" visible="true" format="tabular" assign_primary_output="true"/>
     </data>  
   </outputs>