# HG changeset patch
# User matthias
# Date 1559060405 14400
# Node ID 7050480907b5a2171d9ab219cb3b46201b4c31e1
# Parent  85d952c49c20925c76e04a030ab157058beac532
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit a54770771e567c7ad8a9dd75cc4689c3935ef11c

diff -r 85d952c49c20 -r 7050480907b5 README.md
--- a/README.md	Mon May 27 13:26:40 2019 -0400
+++ b/README.md	Tue May 28 12:20:05 2019 -0400
@@ -11,7 +11,7 @@
 Datatypes
 =========
 
-The dada2 Galaxy wrappers use a few extra data types to ensure that only inputs of the correct type can be used. 
+The dada2 Galaxy wrappers use a few extra data types to ensure that only inputs of the correct type can be used, these datatypes are available from Galaxy release 19.05, for earlier releases they need to be added manually. 
 
 For the outputs of derep, dada, learnErrors, and mergePairs the following datatypes are used that derive from  Rdata (which contains the named list that is returned from the corresponding dada function):
 
@@ -35,5 +35,4 @@
 TODOs 
 =====
 
-- implememt getUniques tool to view intermediate results?
-- implement tests for cached reference data
+- implement getUniques tool to view intermediate results?
diff -r 85d952c49c20 -r 7050480907b5 dada2_assignTaxonomyAddspecies.xml
--- a/dada2_assignTaxonomyAddspecies.xml	Mon May 27 13:26:40 2019 -0400
+++ b/dada2_assignTaxonomyAddspecies.xml	Tue May 28 12:20:05 2019 -0400
@@ -130,7 +130,7 @@
     </outputs>
     <tests>
         <!-- test w default params -->
-        <test>
+        <test expect_num_outputs="1">>
             <param name="seqs" ftype="dada2_sequencetable" value="removeBimeraDenovo_F3D0.tab"/>
             <param name="reference_cond|reference_select" value="history"/>
             <param name="reference_cond|refFasta" ftype="fasta" value="reference.fa"/>
@@ -140,8 +140,18 @@
             <param name="addSpecies_cond|speciesreference_cond|speciesrefFasta" ftype="fasta" value="reference_species.fa" />
             <output name="output" value="assignTaxonomyAddspecies_F3D0.tab" ftype="tabular" />
         </test>
-        <!-- test w output bootstraps, minRC -->
-        <test>
+         <!-- test w default params, bulit in reference -->
+        <test expect_num_outputs="1">
+            <param name="seqs" ftype="dada2_sequencetable" value="removeBimeraDenovo_F3D0.tab"/>
+            <param name="reference_cond|reference_select" value="builtin"/>
+            <param name="reference_cond|refFasta" value="test_buildid"/>
+            <param name="addSpecies_cond|addSpecies_select" value="TRUE"/>
+            <param name="addSpecies_cond|speciesreference_cond|speciesreference_select" value="builtin"/>
+            <param name="addSpecies_cond|speciesreference_cond|speciesrefFasta" value="test_buildid" />
+            <output name="output" value="assignTaxonomyAddspecies_F3D0.tab" ftype="tabular" />
+        </test>
+        <!-- test w output bootstraps, minRC, note: sim_size for bootstraps output due to the probabilistics -->
+        <test expect_num_outputs="2">
             <param name="seqs" ftype="dada2_sequencetable" value="removeBimeraDenovo_F3D0.tab"/>
             <param name="reference_cond|reference_select" value="history"/>
             <param name="reference_cond|refFasta" ftype="fasta" value="reference.fa"/>
@@ -155,10 +165,8 @@
             <param name="addSpecies_cond|allowMultiple" value="TRUE"/>
             <param name="addSpecies_cond|tryRC" value="TRUE" />
             <output name="output" value="assignTaxonomyAddspecies_F3D0.tab" ftype="tabular" compare="sim_size" />
-            <output name="bootstraps" value="assignTaxonomyAddspecies_F3D0_boot.tab" ftype="tabular" />
+            <output name="bootstraps" value="assignTaxonomyAddspecies_F3D0_boot.tab" ftype="tabular" compare="sim_size" />
         </test>
-
-        <!-- TODO test with builtin reference -->
     </tests>
     <help><![CDATA[
 Description
diff -r 85d952c49c20 -r 7050480907b5 macros.xml
--- a/macros.xml	Mon May 27 13:26:40 2019 -0400
+++ b/macros.xml	Tue May 28 12:20:05 2019 -0400
@@ -26,7 +26,7 @@
     <token name="@DADA_UNIQUES@">dada2_derep,dada2_dada,dada2_mergepairs</token>
 
     <!-- function to read dada2 data types
-         - derep, dada, and mergepairs are simply read as RDS 
+         - derep, dada, and mergepairs are simply read as RDS
          - sequence_table is a named integer matrix (rows=samples, columns=ASVs)
          - uniques is a named integer vector (columns=ASVs, only one rows)-->
     <token name="@READ_FOO@"><![CDATA[
@@ -48,7 +48,7 @@
     #end def
     ]]></token>
     <!-- function to write dada2 data types (the content or the R variable 'out' is written)
-         - derep, dada, and mergepairs are written as RDS 
+         - derep, dada, and mergepairs are written as RDS
          - sequence_table is a named integer matrix (rows=samples, columns=ASVs)
          - uniques is a named integer vector (columns=ASVs, only one rows)-->
     <token name="@WRITE_FOO@"><![CDATA[
@@ -61,7 +61,27 @@
         saveRDS(data, file=fname)
     }
 }
-    ]]></token> 
+    ]]></token>
+
+    <xml name="fastq_input" token_multiple="" token_collection_type="" token_argument_fwd="" token_argument_rev="">
+        <conditional name="paired_cond">
+            <param name="paired_select" type="select" label="Paired reads">
+                <option value="paired">paired - in a data set pair</option>
+                <option value="separate">paired - in two separate data sets</option>
+                <option value="single">single</option>
+            </param>
+            <when value="paired">
+                <param name="reads" argument="@ARGUMENT_FWD@/@ARGUMENT_REV@" type="data_collection" collection_type="@COLLECTION_TYPE@" format="fastq,fastq.gz" label="Paired short read data"/>
+            </when>
+            <when value="separate">
+                <param name="reads" argument="@ARGUMENT_FWD@" type="data" format="fastq,fastq.gz" multiple="@MULTIPLE@" label="Forward read data"/>
+                <param name="sdaer" argument="@ARGUMENT_REV@" type="data" format="fastq,fastq.gz" multiple="@MULTIPLE@" label="Reverse read data"/>
+            </when>
+            <when value="single">
+                <param name="reads" argument="@ARGUMENT_FWD@" type="data" format="fastq,fastq.gz" multiple="@MULTIPLE@" label="Short read data"/>
+            </when>
+        </conditional>
+    </xml>
 
     <!-- for filterAndTrim -->
     <xml name="trimmers">
@@ -69,7 +89,7 @@
             <param argument="truncQ" type="integer" value="2" min="0" label="Truncate reads at quality threshold" help="Truncate reads at the first instance of a quality score less than or equal to this threshold"/>
             <param argument="trimLeft" type="integer" value="0" min="0" label="Trim start of each read" help="The number of nucleotides to remove from the start of each read."/>
             <param argument="trimRight" type="integer" value="0" min="0" label="Trim end of each read" help="The number of nucleotides to remove from the end of each read"/>
-			<param argument="truncLen" type="integer" value="0" min="0" label="Truncate read length" help="Truncate reads after this amount of bases. Reads shorter than this are discarded. (default 0: no truncation)"/>
+            <param argument="truncLen" type="integer" value="0" min="0" label="Truncate read length" help="Truncate reads after this amount of bases. Reads shorter than this are discarded. (default 0: no truncation)"/>
         </section>
     </xml>
     <xml name="filters">
diff -r 85d952c49c20 -r 7050480907b5 test-data/dada2_species.loc
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/dada2_species.loc	Tue May 28 12:20:05 2019 -0400
@@ -0,0 +1,10 @@
+# This is a sample file distributed with Galaxy that is used to define a
+# list of dada2 reference data sets for species assignment, using three
+# tab separated columns:
+#
+# <unique_build_id>	<display_name>	<fasta_file_path>
+#
+# Datasets can be retrieved from http://busco.ezlab.org/frame_wget.html
+#
+# Datasets can be retrieved from https://benjjneb.github.io/dada2/training.html
+test_buildid	test_displayname	${__HERE__}/reference_species.fa
diff -r 85d952c49c20 -r 7050480907b5 test-data/dada2_taxonomy.loc
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/dada2_taxonomy.loc	Tue May 28 12:20:05 2019 -0400
@@ -0,0 +1,10 @@
+# This is a sample file distributed with Galaxy that is used to define a
+# list of dada2 reference data sets for taxonomy assignment, using three
+# tab separated columns:
+#
+# <unique_build_id>	<display_name>	<fasta_file_path>	<taxlevels>
+#
+# Datasets can be retrieved from https://benjjneb.github.io/dada2/training.html
+# 
+# taxlevels is a comma separated list of taxonomy levels
+test_buildid	test_displayname	${__HERE__}/reference.fa	Level1,Level2,Level3,Level4,Level5
diff -r 85d952c49c20 -r 7050480907b5 test-data/qualityProfile.pdf
Binary file test-data/qualityProfile.pdf has changed
diff -r 85d952c49c20 -r 7050480907b5 test-data/qualityProfileMultiple.pdf
Binary file test-data/qualityProfileMultiple.pdf has changed
diff -r 85d952c49c20 -r 7050480907b5 test-data/qualityProfileMultiple_rev.pdf
Binary file test-data/qualityProfileMultiple_rev.pdf has changed
diff -r 85d952c49c20 -r 7050480907b5 test-data/qualityProfileSmallSample.pdf
Binary file test-data/qualityProfileSmallSample.pdf has changed
diff -r 85d952c49c20 -r 7050480907b5 test-data/qualityProfile_rev.pdf
Binary file test-data/qualityProfile_rev.pdf has changed
diff -r 85d952c49c20 -r 7050480907b5 tool_data_table_conf.xml.test
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test	Tue May 28 12:20:05 2019 -0400
@@ -0,0 +1,11 @@
+<?xml version="1.0"?>
+<tables>
+    <table name="dada2_species" comment_char="#">
+        <columns>value, name, path</columns>
+        <file path="${__HERE__}/test-data/dada2_species.loc" />
+    </table>
+    <table name="dada2_taxonomy" comment_char="#">
+        <columns>value, name, path, taxlevels</columns>
+        <file path="${__HERE__}/test-data/dada2_taxonomy.loc" />
+    </table>
+</tables>