# HG changeset patch
# User iuc
# Date 1638005760 0
# Node ID 95ab864b281ae785c1de56789941408904c1cf67
# Parent  2595c27071c202b895f7ed9ed58e489873bb60f0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kma commit a3fc5e6a1731ed2a63aed6b4c3e858bf4d9beecd"

diff -r 2595c27071c2 -r 95ab864b281a kma_map.xml
--- a/kma_map.xml	Sat Feb 15 15:32:58 2020 -0500
+++ b/kma_map.xml	Sat Nov 27 09:36:00 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="kma_map" name="Map with KMA" version="@TOOL_VERSION@+galaxy0">
+<tool id="kma_map" name="Map with KMA" version="@TOOL_VERSION@+galaxy1">
     <description></description>
     <macros>
         <import>macros.xml</import>
@@ -11,7 +11,7 @@
         <![CDATA[
         kma
             -t \${GALAXY_SLOTS:-1}
-	    -t_db '${kma_index.fields.path}'
+            -t_db '${kma_index.fields.path}'
             #if $single_paired.single_paired_selector == 'paired'
                 -ipe '${single_paired.forward_input}' '${single_paired.reverse_input}'
             #elif $single_paired.single_paired_selector == "paired_collection":
@@ -26,6 +26,7 @@
               #if str($settings.p_value)
                 -p '${settings.p_value}'
               #end if
+              $settings.exhaustive_mode
               ${settings.decontaminate}
               ${settings.dense}
               ${settings.ref_fsa}
@@ -60,12 +61,13 @@
                 -gapextend '${settings.gapextend}'
               #end if
               ${settings.force_end_to_end}
+              -per $settings.pairing_reward
               ${settings.set_cge_penalties_and_rewards}
             #end if
             -o output
 	 
         #if str($settings.advanced) == "advanced" and $settings.matrix
-            && gunzip output.mat.gz
+          && gunzip output.mat.gz
         #end if
         && gunzip output.frag.gz
 	]]>
@@ -78,17 +80,17 @@
                 <option selected="True" value="single">Single-end data</option>
             </param>
             <when value="paired_collection">
-                <param format="@INTYPES@" name="input_pair" type="data_collection" collection_type="paired" label="Collection of paired reads" help="FASTQ datasets" />
+                <param argument="-ipe" format="@INTYPES@" name="input_pair" type="data_collection" collection_type="paired" label="Collection of paired reads" help="FASTQ datasets" />
             </when>
             <when value="paired">
-                <param format="@INTYPES@" name="forward_input" type="data" label="Forward strand" help="FASTQ dataset"/>
-                <param format="@INTYPES@" name="reverse_input" type="data" label="Reverse strand" help="FASTQ dataset"/>
+                <param argument="-ipe" format="@INTYPES@" name="forward_input" type="data" label="Forward strand" help="FASTQ dataset"/>
+                <param argument="-ipe" format="@INTYPES@" name="reverse_input" type="data" label="Reverse strand" help="FASTQ dataset"/>
             </when>
             <when value="single">
-                <param format="@INTYPES@" label="Input sequences" name="input_sequences" type="data" help="FASTQ datasets"/>
+                <param argument="-i" format="@INTYPES@" label="Input sequences" name="input_sequences" type="data" help="FASTQ datasets"/>
             </when>
         </conditional>
-        <param name="kma_index" type="select">
+        <param argument="-t_db" name="kma_index" type="select">
             <options from_data_table="kma_index">
                 <validator type="no_options" message="No KMA index available" />
             </options>
@@ -101,27 +103,27 @@
             <when value="simple">
             </when>
             <when value="advanced">
-                <param name="kmer_size" type="integer" min="4" value="16" max="32" label="Kmer Size" />
-                <param name="p_value" type="float" min="0.0" value="0.05" max="1.0" label="p-value"/>
-                <param name="exhaustive_mode" type="boolean" truevalue="-ex_mode" falsevalue="" label="Exhaustive Mode" />
-                <param name="decontaminate" type="boolean" truevalue="-deCon" falsevalue="" label="Decontaminate" />
-                <param name="dense" type="boolean" truevalue="-dense" falsevalue="" label="Do not allow insertions in assembly" />
-                <param name="ref_fsa" type="boolean" truevalue="-ref_fsa" falsevalue="" label="Consensus sequence has 'n' instead of gaps" />
-                <param name="matrix" type="boolean" truevalue="-matrix" falsevalue="" label="Output assembly matrix" />
-                <param name="all_best_mappings" type="boolean" truevalue="-a" falsevalue="" label="Print all best mappings" />
-                <param name="minimum_phred_score" type="integer" min="0" value="20" max="60" label="Minimum phred score" />
-                <param name="cut_5_prime" type="integer" min="0" value="0" max="64" label="Cut a constant number of nucleotides from the 5 prime" />
-                <param name="only_count_kmers" type="boolean" truevalue="-Sparse" falsevalue="" label="Only count kmers" />
-                <param name="min_id" type="float" min="0.0" value="1.0" max="100.0" label="Minimum percent identity"/>
-                <param name="force_end_to_end" type="boolean" truevalue="-1t1" falsevalue="" label="Force end to end mapping" />
-                <param name="base_call_depth" type="integer" min="1" value="1" max="1000" label="Minimum depth at base" />
-                <param name="minimum_mapping_quality" type="integer" min="0" value="0" max="100" label="Minimum mapping quality" />
-                <param name="reward" type="integer" min="1" value="1" max="100" label="Score for match" />
-                <param name="penalty" type="integer" min="-100" value="-2" max="0" label="Penalty for mismatch" />
-                <param name="gapopen" type="integer" min="-100" value="-3" max="0" label="Penalty for gap opening" />
-                <param name="gapextend" type="integer" min="-100" value="-1" max="0" label="Penalty for gap extension" />
-                <param name="pairing_reward" type="integer" min="1" value="7" max="100" label="Reward for pairing reads" />
-                <param name="set_cge_penalties_and_rewards" type="boolean" truevalue="-cge" falsevalue="" label="Set CGE penalties and rewards" />
+                <param argument="-k" name="kmer_size" type="integer" min="4" value="16" max="32" label="Kmer Size" />
+                <param argument="-p" name="p_value" type="float" min="0.0" value="0.05" max="1.0" label="p-value"/>
+                <param argument="-ex_mode" name="exhaustive_mode" type="boolean" truevalue="-ex_mode" falsevalue="" label="Exhaustive Mode" />
+                <param argument="-deCon" name="decontaminate" type="boolean" truevalue="-deCon" falsevalue="" label="Decontaminate" />
+                <param argument="-dense" name="dense" type="boolean" truevalue="-dense" falsevalue="" label="Do not allow insertions in assembly" />
+                <param argument="-ref_fsa" name="ref_fsa" type="boolean" truevalue="-ref_fsa" falsevalue="" label="Consensus sequence has 'n' instead of gaps" />
+                <param argument="-matrix" name="matrix" type="boolean" truevalue="-matrix" falsevalue="" label="Output assembly matrix" />
+                <param argument="-a" name="all_best_mappings" type="boolean" truevalue="-a" falsevalue="" label="Print all best mappings" />
+                <param argument="-mp" name="minimum_phred_score" type="integer" min="0" value="20" max="60" label="Minimum phred score" />
+                <param argument="-5p" name="cut_5_prime" type="integer" min="0" value="0" max="64" label="Cut a constant number of nucleotides from the 5 prime" />
+                <param argument="-Sparse" name="only_count_kmers" type="boolean" truevalue="-Sparse" falsevalue="" label="Only count kmers" />
+                <param argument="-ID" name="min_id" type="float" min="0.0" value="1.0" max="100.0" label="Minimum percent identity"/>
+                <param argument="-1t1" name="force_end_to_end" type="boolean" truevalue="-1t1" falsevalue="" label="Force end to end mapping" />
+                <param argument="-bcd" name="base_call_depth" type="integer" min="1" value="1" max="1000" label="Minimum depth at base" />
+                <param argument="-mq" name="minimum_mapping_quality" type="integer" min="0" value="0" max="100" label="Minimum mapping quality" />
+                <param argument="-reward" name="reward" type="integer" min="1" value="1" max="100" label="Score for match" />
+                <param argument="-penalty" name="penalty" type="integer" min="-100" value="-2" max="0" label="Penalty for mismatch" />
+                <param argument="-gapopen " name="gapopen" type="integer" min="-100" value="-3" max="0" label="Penalty for gap opening" />
+                <param argument="-gapextend" name="gapextend" type="integer" min="-100" value="-1" max="0" label="Penalty for gap extension" />
+                <param argument="-per" name="pairing_reward" type="integer" min="1" value="7" max="100" label="Reward for pairing reads" />
+                <param argument="-cge" name="set_cge_penalties_and_rewards" type="boolean" truevalue="-cge" falsevalue="" label="Set CGE penalties and rewards" />
             </when>
         </conditional>
     </inputs>