changeset 0:6053ca7c24f3 draft

"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/chewbbaca commit 66a9f18802686a105b392e73e82c0078d0cdf2a4"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/chewbbaca_schemaevaluator.xml	Fri Jan 24 19:33:33 2020 +0000
@@ -0,0 +1,51 @@
+<tool id="chewbbaca_schemaevaluator" name="chewBBACA SchemaEvaluator" version="@TOOL_VERSION@+galaxy0">
+    <description>BSR-Based Allele Calling Algorithm</description>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">chewbbaca</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        chewBBACA.py SchemaEvaluator
+          --cpu \${GALAXY_SLOTS:-1}
+          -i '${schema}'
+          -t '${threshold}'
+        ]]>
+    </command>
+    <inputs>
+        
+    </inputs>
+
+    <!-- define outputs -->
+    <outputs>
+        <data format="tabular" name="statistics" label="${tool.name}: on ${on_string}: Statistics" />
+        <data format="tabular" name="contigs_info" label="${tool.name}: on ${on_string}: Contigs Info" />
+        <data format="tabular" name="alleles" label="${tool.name}: on ${on_string}: Alleles"  />
+        <data format="txt" name="log" label="${tool.name}: on ${on_string}: Log" />
+        <data format="tabular" name="repeated_loci" label="${tool.name}: on ${on_string}: Repeated Loci" />
+    </outputs>
+    <tests>
+        
+    </tests>
+    <help><![CDATA[
+    ]]>
+    </help>
+    <citations>
+        <citation type="bibtex">
+            @ARTICLE{andrews_s,
+                author = {Rossi, M and Silva, M and Ribeiro-Gonçalves, B and Silva, DN
+                          and Machado, MP and Oleastro, M and Borges, V and Isidro, J
+                          and Gomes, JP and Vieira, L and Barker, DOR and Llarena, AK
+                          and Halkilahti, J and Jaakkonen, A and Palma, F and Culebro, A
+                          and Kivistö, R and Hänninen, ML and Laukkanen-Ninios, R
+                          and Fredriksson-Ahomaa, M and Salmenlinna, S and Hakkinen, M
+                          and Garaizer, J and Bikandi, J and Hilbert, F and Taboada, EN
+                          and Carriço, JA},
+                keywords = {bioinformatics, ngs, mlst},
+                title = {{INNUENDO whole and core genome MLST databases and schemas
+                          for foodborne pathogens}},
+                url = {https://github.com/TheInnuendoProject/chewBBACA_schemas}
+            }
+        </citation>
+      <citation type="doi">10.1099/mgen.0.000166</citation>
+      <citation type="doi">10.1371/journal.pgen.1007261</citation>
+    </citations>
+</tool>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Fri Jan 24 19:33:33 2020 +0000
@@ -0,0 +1,3 @@
+<macros>
+    <token name="@TOOL_VERSION@">2.1.0</token>
+</macros>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/chewbbaca_prodigal_training_files.loc.sample	Fri Jan 24 19:33:33 2020 +0000
@@ -0,0 +1,7 @@
+# Expect three columns, tab separated, as follows:
+# - value (Galaxy records this in the Galaxy DB)
+# - name (Galaxy shows this in the UI)
+# - path to prodigal training file
+#
+# e.g.
+# 408a8d5f-e4a6-4aff-add7-b2aa43302564<tab>E. coli prodigal training file<tab>/path/to/ecoli.ptf

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Fri Jan 24 19:33:33 2020 +0000
@@ -0,0 +1,8 @@
+<?xml version="1.0"?>
+<tables>
+    <!-- Locations of chewbbaca prodigal training files in the required format -->
+    <table name="chewbbaca_prodigal_training_files" comment_char="#">
+        <columns>value, name, path</columns>
+        <file path="tool-data/chewbbaca_prodigal_training_files.loc" />
+    </table>
+</tables>