# HG changeset patch
# User iuc
# Date 1580426285 0
# Node ID 96859e4292cb01d0d4eff85e2cefefdd6b0da3bf
# Parent  a3f95a688c4702fb9dc6415707a6b39b91906768
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snippy commit 25b2375521fec3162644696b67e54f654fab2e79"

diff -r a3f95a688c47 -r 96859e4292cb snippy_clean_full_aln.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/snippy_clean_full_aln.xml	Thu Jan 30 23:18:05 2020 +0000
@@ -0,0 +1,87 @@
+<?xml version="1.0" encoding="utf-8"?>
+<tool id="snippy_clean_full_aln" name="snippy-clean_full_aln" version="@VERSION@+galaxy0">
+    <description>
+        Replace any non-standard sequence characters in snippy 'core.full.aln' file.
+    </description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        snippy-clean_full_aln
+            '${full_aln}'
+            #if $custom_char.custom_char_selector:
+              --to '${custom_char.to_char}'
+            #end if
+            > '${clean_full_aln}'
+    ]]></command>
+
+    <inputs>
+        <param name="full_aln" type="data" format="fasta" label="Snippy core.full.aln file" help="" />
+        <conditional name="custom_char">
+            <param name="custom_char_selector" type="boolean" display="radio" label="Use custom replacement character" />
+            <when value="false" />
+            <when value="true">
+                <param name="to_char" type="text" label="Replacement character" help="Replace non-[AGTCN-] chars with this character, defaults to 'N' if none entered" >
+                    <sanitizer>
+                        <valid initial="string.printable">
+                            <remove value="&apos;" />
+                        </valid>
+                        <mapping initial="none">
+                            <add source="&apos;" target="&apos;&quot;&apos;&quot;&apos;" />
+                        </mapping>
+                    </sanitizer>
+                </param>
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="clean_full_aln" format="fasta" label="${tool.name} on ${on_string} cleaned core alignment" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="full_aln" value="core.full.nonclean.aln" />
+            <output name="clean_full_aln">
+                <assert_contents>
+                    <has_line line="GCNNCG" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="full_aln" value="core.full.nonclean.aln" />
+            <param name="custom_char_selector" value="true" />
+            <param name="to_char" value="X" />
+            <output name="clean_full_aln">
+                <assert_contents>
+                    <has_line line="GCXXCG" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+    The core.full.aln file is a FASTA formatted multiple sequence alignment file. 
+    It has one sequence for the reference, and one for each sample participating 
+    in the core genome calculation. Each sequence has the same length as the reference 
+    sequence.
+
+    Character 	Meaning
+    ATGC 	Same as the reference
+    atgc 	Different from the reference
+    - 	Zero coverage in this sample or a deletion relative to the reference
+    N 	Low coverage in this sample (based on --mincov)
+    X 	Masked region of reference (from --mask)
+    n 	Heterozygous or poor quality genotype (has GT=0/1 or QUAL < --minqual in snps.raw.vcf)
+   
+    You can remove all the "weird" characters and replace them with N using this tool. 
+    This is useful when you need to pass it to a tree-building or recombination-removal 
+    tool:
+
+    ```
+    % snippy-clean_full_aln core.full.aln > clean.full.aln
+    % run_gubbins.py -p gubbins clean.full.aln
+    % snp-sites -c gubbins.filtered_polymorphic_sites.fasta > clean.core.aln
+    % FastTree -gtr -nt clean.core.aln > clean.core.tree
+    ```
+    ]]></help>
+    <expand macro="citations" />
+</tool>
diff -r a3f95a688c47 -r 96859e4292cb test-data/core.full.nonclean.aln
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/core.full.nonclean.aln	Thu Jan 30 23:18:05 2020 +0000
@@ -0,0 +1,4 @@
+>Reference
+CGATGC
+>S1
+GCXXCG