# HG changeset patch
# User Michael R. Crusoe <mcrusoe@msu.edu>
# Date 1404049657 14400
# Node ID cec78b57476043a7ed43aed784d37c75c800d8b0
# Parent  d00e18a0a3f2f3c8a0a6300f77f908b6f75c2a65
Actually import the macros

diff -r d00e18a0a3f2 -r cec78b574760 abundance-dist-single.xml
--- a/abundance-dist-single.xml	Sun Jun 29 09:22:32 2014 -0400
+++ b/abundance-dist-single.xml	Sun Jun 29 09:47:37 2014 -0400
@@ -9,6 +9,7 @@
 	</description>
 	<macros>
 		<token name="@BINARY@">abundance-dist-single.py</token>
+		<import>macros.xml</import>
 	</macros>
 	<expand macro="requirements" />
 	<command>
diff -r d00e18a0a3f2 -r cec78b574760 abundance-dist.xml
--- a/abundance-dist.xml	Sun Jun 29 09:22:32 2014 -0400
+++ b/abundance-dist.xml	Sun Jun 29 09:47:37 2014 -0400
@@ -1,5 +1,5 @@
 <tool	id="gedlab-khmer-normalize-by-median"
-	name="Abundance Dist"
+	name="Abundance Distribution"
 	version="1.1-1"
 	force_history_refresh="true">
 	
@@ -8,7 +8,8 @@
 		file using a pre-made k-mer counting table.
 	</description>
         <macros>
-                <token name="@BINARY@">abundance-dist-single.py</token>
+		<token name="@BINARY@">abundance-dist-single.py</token>
+		<import>macros.xml</import>
         </macros>
         <expand macro="requirements" />
 	<command>
diff -r d00e18a0a3f2 -r cec78b574760 count-median.xml
--- a/count-median.xml	Sun Jun 29 09:22:32 2014 -0400
+++ b/count-median.xml	Sun Jun 29 09:47:37 2014 -0400
@@ -9,7 +9,8 @@
 		estimate expression levels (mRNAseq) or coverage (genomic/metagenomic).
 	</description>
         <macros>
-                <token name="@BINARY@">count-median.py</token>
+		<token name="@BINARY@">count-median.py</token>
+		<import>macros.xml</import>
         </macros>
         <expand macro="requirements" />
 	<command>
diff -r d00e18a0a3f2 -r cec78b574760 filter-abund.xml
--- a/filter-abund.xml	Sun Jun 29 09:22:32 2014 -0400
+++ b/filter-abund.xml	Sun Jun 29 09:47:37 2014 -0400
@@ -7,37 +7,23 @@
 		Trims fastq/fasta sequences at k-mers of a given abundance
 		based on a provided k-mer counting table.
 	</description>
-
-	<requirements>
-		<requirement
-			type="package"
-			version="1.1">
-				khmer
-		</requirement>
-    	</requirements>
-	
-	<version_command>
-		filter-abund.py --version
-    	</version_command>
-
+	<macros>
+		<token name="@BINARY@">filter-abund.py</token>
+		<import>macros.xml</import>
+	</macros>
+	<expand macro="requirements" />
 	<command>
 		mkdir output; cd output;
 		filter-abund.py
 		$variable_coverage
-		$presencetable_to_load
+		$countingtable_to_load
 		#for input in $inputs
 			$input
 		#end for
 	</command>
 
 	<inputs>
-		<param	name="inputs"
-			multiple="true"
-			type="data"
-			format="fasta,fastq,fastqsanger,fastqsolexa,fastqillumina"
-			label="FAST[AQ] file(s)"
-			help="Put in order of precedence such as longest reads first." />
-
+		<expand macro="multifile-fastaq-inputs" />
 		<param	name="variable_coverage"
 			type="boolean"
 			checked="false"
@@ -45,19 +31,10 @@
 			falsevalue=""
 			label="Variable coverage"
 			help="Only trim when a sequence has high enough coverage (median abundance > 20)" />
-
-		<param	name="presencetable_to_load"
-			type="data"
-			optional="false"
-			label="the khmer abundance table to load"
-			help="The inputs file(s) will be processed using the kmer counts in the specified k-mer counting table file." />
+		<expand macro="input_counting_table_filename" />	
 	</inputs>
 	<outputs>
-		<data	name="output"
-			format="input"
-			label="${tool.name} processed nucleotide sequence file">
-			<discover_datasets pattern="__name__" directory="output" visible="true"/>
-		</data>
+		<expand macro="output_sequences" />
 	</outputs>
  	<stdio>
         <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
diff -r d00e18a0a3f2 -r cec78b574760 macros.xml
--- a/macros.xml	Sun Jun 29 09:22:32 2014 -0400
+++ b/macros.xml	Sun Jun 29 09:47:37 2014 -0400
@@ -68,6 +68,14 @@
 			</when>
 		</conditional>
 	</xml>
+	<xml name="input_sequences_filenames">
+                <param  name="inputs"
+                        multiple="true"
+                        type="data"
+                        format="fasta,fastq,fastqsanger,fastqsolexa,fastqillumina"
+                        label="FAST[AQ] file(s)"
+                        help="Put in order of precedence such as longest reads first." />
+	</xml>
 	<xml name="input_sequence_filename">
                 <param  name="input_sequence_filename"
                         type="data"
@@ -89,4 +97,11 @@
                         k-mers.">
                 </data>
 	</xml>
+	<xml name="output_sequences">
+                <data   name="output"
+                        format="input"
+                        label="${tool.name} processed nucleotide sequence file">
+                        <discover_datasets pattern="__name__" directory="output" visible="true"/>
+                </data>
+	</xml>
 </macros>
diff -r d00e18a0a3f2 -r cec78b574760 normalize-by-median.xml
--- a/normalize-by-median.xml	Sun Jun 29 09:22:32 2014 -0400
+++ b/normalize-by-median.xml	Sun Jun 29 09:47:37 2014 -0400
@@ -7,19 +7,11 @@
 		Filters a fastq/fasta file using digital normalization via
 	    	median k-mer abundances.
 	</description>
-
-	<requirements>
-		<requirement
-			type="package"
-			version="1.1">
-				khmer
-		</requirement>
-    	</requirements>
-	
-	<version_command>
-		normalize-by-median.py --version
-    	</version_command>
-
+        <macros>
+                <token name="@BINARY@">normalize-by-median.py</token>
+                <import>macros.xml</import>
+        </macros>
+        <expand macro="requirements" />
 	<command>
 		mkdir output;
 		cd output;
@@ -48,13 +40,7 @@
 	</command>
 
 	<inputs>
-		<param	name="inputs"
-			multiple="true"
-			type="data"
-			format="fasta,fastq,fastqsanger,fastqsolexa,fastqillumina"
-			label="FAST[AQ] file(s)"
-			help="Put in order of precedence such as longest reads first." />
-
+		<expand macro="input_sequences_filenames" />
 		<param	name="paired_switch"
 			type="boolean"
 			checked="false"
@@ -137,12 +123,7 @@
 			label="${tool.name} k-mer counting table from  #echo ', '.join(map(str, $inputs ))#">
 			<filter>save_countingtable == True</filter>
 		</data>
-		<data	name="outputs"
-			format="input"
-			label="${tool.name} processed nucleotide sequence file">
-			<discover_datasets pattern="__name__" directory="output" visible="true"/>
-		</data>
-
+		<expand macro="output_sequences" />
 	</outputs>
  	<stdio>
         <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->