--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/migmap.xml.orig	Wed Sep 01 07:38:25 2021 +0000
@@ -0,0 +1,141 @@
+<<<<<<< HEAD
+<tool id="migmap" name="MiGMAP" version="@TOOL_VERSION@+galaxy2" profile="20.01">
+    <description>mapper for full-length T- and B-cell repertoire sequencing
+    </description>
+=======
+<tool id="migmap" name="MiGMAP" version="@TOOL_VERSION@+galaxy1">
+    <description>mapper for full-length T- and B-cell repertoire sequencing</description>
+    <xrefs>
+        <xref type='bio.tools'>MiGMAP</xref>
+    </xrefs>
+>>>>>>> d4217b609 (add bio.tools IDs until M)
+    <macros>
+        <token name="@TOOL_VERSION@">1.0.3</token>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">migmap</requirement>
+    </requirements>
+    <command detect_errors='aggressive'><![CDATA[
+export IGBLAST_PATH=\$(dirname \$(which igblastn)) &&
+mkdir -p temp_db/igblast &&
+ln -s "\${IGBLAST_PATH}/../share/igblast/bin/" ./temp_db/igblast &&
+ln -s "\${IGBLAST_PATH}/../share/igblast/internal_data/" ./temp_db/igblast &&
+ln -s "\${IGBLAST_PATH}/../share/igblast/optional_file/" ./temp_db/igblast &&
+
+#if $input.is_of_type('fasta') :
+    ln -s '$input' in.fa &&
+#else if $input.is_of_type('fasta.gz') :
+    ln -s '$input' in.fa.gz &&
+#else if $input.is_of_type('fastq') :
+    ln -s '$input' in.fq &&
+#else if $input.is_of_type('fastq.gz') :
+    ln -s '$input' in.fq.gz
+#end if
+
+migmap 
+    $allow_incomplete
+    $allow_no_cdr3
+    $allow_noncanonical
+    $allow_noncoding
+    $all_alleles
+    $by_read
+    #if str($qual_threshold):
+        -q $qual_threshold
+    #end if
+    -p "\${GALAXY_SLOTS:-4}"
+    --data-dir ./temp_db/igblast/
+    -S $species 
+    -R $receptor_list
+    #if $input.is_of_type('fasta'): 
+        in.fa
+    #else
+        in.fq
+    #end if
+    '$output'
+    ]]></command>
+    <inputs>
+        <param type="data" name="input" format="fasta,fastq"/>
+        <param type="select" name="species" label="Species" value='human'>
+            <option value='human' selected='true'>Human</option>
+            <option value='mouse'>Mouse</option>
+            <option value='rat'>Rat</option>
+            <option value='rabbit'>Rabbit</option>
+            <option value='rhesus_monkey'>Rhesus monkey</option>
+        </param>
+        <param type="select" name="receptor_list" label="Receptor and Chain" multiple='true' value='IGH'>
+            <option value='IGH' selected='true'>IGH</option>
+            <option value='IGL'>IGL</option>
+            <option value='IGK'>IGK</option>
+            <option value='TRA'>TRA</option>
+            <option value='TRB'>TRB</option>
+            <option value='TRG'>TRG</option>
+            <option value='TRD'>TRD</option>
+        </param>
+        <param name="qual_threshold" type="integer" label="Quality Theshold" optional="true"
+           help="Threshold for average quality of mutations and N-regions of CDR3 (only relevant for fastq input)"/>
+        <param name="allow_incomplete" type="boolean" label="Report clonotypes with partial CDR3 mapping" checked="false"
+           truevalue="--allow-incomplete" falsevalue=""/>
+        <param name="all_alleles" type="boolean"
+           label="use all alleles during alignemt (default = only major (*01) alleles)" checked='false'
+           truevalue="--all-alleles" falsevalue=""/>
+        <param name="allow_no_cdr3" type="boolean" label="Report clonotypes with no CDR3" checked='false'
+           truevalue="--allow-no-cdr3" falsevalue=""/>
+        <param name="allow_noncanonical" type="boolean" label="Report clonotypes that have non-canonical CDR3"
+           checked='false'
+           truevalue="--allow-noncanonical" falsevalue=""/>
+        <param name="allow_noncoding" type="boolean" label="Report non-coding clonotypes (stop codon or frameshift)"
+           checked='false'
+           truevalue="--allow-noncoding" falsevalue=""/>
+        <param name="by_read" type="boolean" label="Report mapping details for each read" checked='false'
+           truevalue="--by-read" falsevalue=""/>
+    </inputs>
+    <outputs>
+        <data name="output" format="tabular"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="test_stop_codon.fa"/>
+            <param name="allow_noncoding" value="--allow-noncoding"/>
+            <param name="by_read" value="--by-read"/>
+            <param name="allow_noncanonical" value="--allow-noncanonical"/>
+            <param name="allow_no_cdr3" value="--allow-no-cdr3"/>
+            <param name="allow_incomplete" value="--allow-incomplete"/>
+            <param name="all_alleles" value="--all-alleles"/>
+            <output name="output" file="test_stop_codon.out"/>
+        </test>
+        <test>
+            <param name="input" value="test_stop_codon.fq.gz" ftype="fastqsanger.gz"/>
+            <param name="allow_noncoding" value="--allow-noncoding"/>
+            <param name="by_read" value="--by-read"/>
+            <param name="allow_noncanonical" value="--allow-noncanonical"/>
+            <param name="allow_no_cdr3" value="--allow-no-cdr3"/>
+            <param name="allow_incomplete" value="--allow-incomplete"/>
+            <param name="all_alleles" value="--all-alleles"/>
+            <output name="output" file="test_stop_codon.out" lines_diff="2"/>
+        </test>
+        <test>
+            <param name="allow_noncoding" value="--allow-noncoding"/>
+            <param name="by_read" value="--by-read"/>
+            <param name="input" value="test_out_of_frame.fa"/>
+            <output name="output" file="test_out_of_frame.out"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+    This software is a smart wrapper for the IgBlast V-(D)-J mapping tool designed to facilitate analysis immune
+    receptor libraries profiled using high-throughput sequencing
+
+    ]]></help>
+    <citations>
+        <citation type="bibtex">
+          @misc{githubmigmap,
+          author = {Shugay, Mikhail},
+          year = {2015},
+          title = {migmap},
+          publisher = {GitHub},
+          journal = {GitHub repository},
+          url = {https://github.com/mikessh/migmap},
+          }
+        </citation>
+    </citations>
+</tool>