Mercurial > repos > matthias > dada2_makesequencetable

changeset 9:6da167015b3e draft

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planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit a54770771e567c7ad8a9dd75cc4689c3935ef11c
author matthias
date Tue, 28 May 2019 12:19:29 -0400
parents 54f6cd01b02e
children 2f9e68f9c033
files README.md macros.xml test-data/dada2_species.loc test-data/dada2_taxonomy.loc test-data/qualityProfile.pdf test-data/qualityProfileMultiple.pdf test-data/qualityProfileMultiple_rev.pdf test-data/qualityProfileSmallSample.pdf test-data/qualityProfile_rev.pdf tool_data_table_conf.xml.test
diffstat 10 files changed, 57 insertions(+), 7 deletions(-) [+]
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--- a/README.md	Mon May 27 13:26:04 2019 -0400
+++ b/README.md	Tue May 28 12:19:29 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?
--- a/macros.xml	Mon May 27 13:26:04 2019 -0400
+++ b/macros.xml	Tue May 28 12:19:29 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">
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/dada2_species.loc	Tue May 28 12:19:29 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
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/dada2_taxonomy.loc	Tue May 28 12:19:29 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	${__HERE__}/reference.fa	Level1,Level2,Level3,Level4,Level5
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Binary file test-data/qualityProfileMultiple.pdf has changed
Binary file test-data/qualityProfileMultiple_rev.pdf has changed
Binary file test-data/qualityProfileSmallSample.pdf has changed
Binary file test-data/qualityProfile_rev.pdf has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test	Tue May 28 12:19:29 2019 -0400
@@ -0,0 +1,11 @@
+<?xml version="1.0"?>
+<tables>
+    <table name="dada2_species" comment_char="#">
+        <columns>value, name, path</columns>
+        <file path="${__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>