--- a/mykrobe_predict.xml	Thu Aug 26 20:37:45 2021 +0000
+++ b/mykrobe_predict.xml	Wed Sep 01 07:46:02 2021 +0000
@@ -1,5 +1,8 @@
 <tool id="mykrobe_predict" name="mkyrobe predict" version="@TOOL_VERSION@.1+galaxy0"  profile="@PROFILE@">
     <description>Antibiotic resistance predictions</description>
+    <xrefs>
+        <xref type="bio.tools">Mykrobe</xref>
+    </xrefs>
     <macros>
         <import>macro.xml</import>
     </macros>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mykrobe_predict.xml.orig	Wed Sep 01 07:46:02 2021 +0000
@@ -0,0 +1,154 @@
+<<<<<<< HEAD
+<tool id="mykrobe_predict" name="mkyrobe predict" version="@TOOL_VERSION@.1+galaxy0"  profile="@PROFILE@">
+    <description>Antibiotic resistance predictions</description>
+=======
+<tool id="mykrobe_predict" name="mkyrobe predict" version="0.7.0">
+    <description>Antibiotic resistance predictions</description>
+    <xrefs>
+        <xref type='bio.tools'>Mykrobe</xref>
+    </xrefs>
+>>>>>>> 84b0f9990 (add bio.tools IDs until M)
+    <macros>
+        <import>macro.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+<<<<<<< HEAD
+    <command detect_errors="exit_code"><![CDATA[
+#import difflib
+#import re
+=======
+    <command detect_errors="exit_code">
+<![CDATA[
+        @select_inputs@
+>>>>>>> 84b0f9990 (add bio.tools IDs until M)
+
+mykrobe predict
+--species '${select_species.species}'
+--panel '${select_species.panel}'
+
+#if $conf_percent_cutoff:
+    --conf_percent_cutoff '${conf_percent_cutoff}'
+#end if
+
+#if $min_depth:
+    --min_depth ${min_depth}
+#end if
+
+@shared_options@
+
+-q
+-t "\${GALAXY_SLOTS:-1}"
+
+#if $data_type.type in ["single", "paired"]:
+    #set read1 = $data_type.seq1
+    #set read1_identifier = re.sub('[^\s\w\-]', '_', str($read1.element_identifier))
+    #if $data_type.type == "single":
+        --sample '${read1_identifier}'
+    --seq '${read1}'
+    #else:
+        #set read2 = $data_type.seq2
+        #set read2_identifier = re.sub('[^\s\w\-]', '_', str($read2.element_identifier))
+        #set matches = difflib.SequenceMatcher(None, read1_identifier, read2_identifier).get_matching_blocks()
+        #set match = $matches[0]
+        #set identifier = re.sub('[^\s\w\-]', '_', str($read1_identifier[match.a:match.a + match.size]))
+    --sample '${identifier}'
+    --seq '${read1}' '${read2}'
+    #end if
+#elif $data_type.type == "collection":
+    #set identifier = re.sub('[^\s\w\-]', '_', str($data_type.collection1.element_identifier))
+    --sample '${identifier}'
+    --seq '${data_type.collection1.forward}' '${data_type.collection1.reverse}'
+#end if
+
+--format '${format}'
+
+> '$output']]>
+    </command>
+    <inputs>
+        <expand macro="inputs"/>
+        <conditional name="select_species">
+            <param name="species" type="select" label="Specify Species for AMR">
+                <option value="tb">Mycobacterium tuberculosis (tb)</option>
+                <option value="staph">Staphylococcus aureus (staph)</option>
+                <option value="sonnei">Shigella sonnei (sonnei)</option>
+            </param>
+            <when value="staph">
+                <param name="panel" type="select" label="Select panel for Staph only">
+                    <option value="20170217">20170217</option>
+                </param>
+            </when>
+            <when value="tb">
+                <param name="panel" type="select" label="Select panel for TB only">
+                    <option value="202010">202010</option>
+                    <option value="201901">201901</option>
+                    <option value="bradley-2015">Bradely 2015</option>
+                </param>
+            </when>
+            <when value="sonnei">
+                <param name="panel" type="select" label="Select panel for sonnei only">
+                    <option value="20210201">20210201</option>
+                    <option value="20201012">20201012</option>
+                </param>
+            </when>
+        </conditional>
+        <param argument="--min_depth" optional="True" type="integer" min="0" label="Minimum depth"  help=""/>
+        <param argument="--conf_percent_cutoff" optional="True" type="integer" label="Confidence percent cutoff" help="Number between 0 and 100. Determines --min_variant_conf, by simulating variants and choosing the cutoff that would keep x% of the variants. Default is 90 if --ont, otherwise --min_variant_conf is used as the cutoff">
+            <validator type="in_range" min="0" max="100" message="Confidence percent cutoff should be between 0 and 100" />
+        </param>
+        <expand macro="options"/>
+        <param argument="--format" type="select" label="Select the prefered output format">
+            <option value="csv" >csv</option>
+            <option value="json">json</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="output" format="csv" label="prediction">
+            <change_format>
+                <when input="format" value="json" format="json"/>
+            </change_format>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="type" value="single"/>
+            <param name="seq1" ftype="fastq" value="reads.fastq"/>
+            <param name="species" value="tb"/>
+            <param name="panel" value="bradley-2015"/>
+            <param name="format" value="json"/>
+            <output name="output">
+                <assert_contents>
+                    <has_text_matching expression="susceptibility"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="type" value="single"/>
+            <param name="seq1" ftype="fastq" value="reads.fastq"/>
+            <param name="species" value="sonnei"/>
+            <param name="panel" value="20201012"/>
+            <param name="format" value="json"/>
+            <output name="output">
+                <assert_contents>
+                    <has_text_matching expression="susceptibility"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="type" value="single"/>
+            <param name="seq1" ftype="fastq.gz" value="reads.fastq.gz"/>
+            <param name="species" value="sonnei"/>
+            <param name="panel" value="20201012"/>
+            <param name="format" value="json"/>
+            <output name="output">
+                <assert_contents>
+                    <has_text_matching expression="susceptibility"/>
+              </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help>
+        @ATTRIBUTION@
+    </help>
+    <expand macro="citation" />
+</tool>
+