From 620e12d364148a0fbe8c60820a3c0a0f7c1561b9 Mon Sep 17 00:00:00 2001
From: Calvin Morrison <mutantturkey@gmail.com>
Date: Thu, 19 Jun 2014 10:41:38 -0400
Subject: working multifasta2otu

---
 src/galaxy/multifasta2otu.xml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

(limited to 'src/galaxy')

diff --git a/src/galaxy/multifasta2otu.xml b/src/galaxy/multifasta2otu.xml
index b80f8b2..eebe246 100644
--- a/src/galaxy/multifasta2otu.xml
+++ b/src/galaxy/multifasta2otu.xml
@@ -1,10 +1,10 @@
 <tool id="multifasta" name="Multifasta">
 	<description>Get Abundances on Multiple Files</description>
-	<command interpreter="bash">multifasta_to_otu -k $kmer -s $db -f &lt;( echo
+	<command>bash -c "multifasta_to_otu -k $kmer -s $db -f &lt;( echo
 #for $input in $inputs:
-"${input}"
+${input}
 #end for
- | xargs -n 1	) -o $output</command>
+ | xargs -n 1	) -o $output"</command>
 	<inputs>
 		<param name="inputs" multiple="true" type="data" format="fasta" label="input fasta"/>
 		<param name="db" type="data" format="data" label="trained database"/>
-- 
cgit v1.2.3


From 62067f0ca6db19fcdedc84476e68ba3864062f54 Mon Sep 17 00:00:00 2001
From: Calvin Morrison <mutantturkey@gmail.com>
Date: Thu, 19 Jun 2014 11:05:42 -0400
Subject: remove help flags

---
 src/galaxy/quikr.xml       | 20 ++------------------
 src/galaxy/quikr_train.xml | 18 ------------------
 2 files changed, 2 insertions(+), 36 deletions(-)

(limited to 'src/galaxy')

diff --git a/src/galaxy/quikr.xml b/src/galaxy/quikr.xml
index 89729be..65d604b 100644
--- a/src/galaxy/quikr.xml
+++ b/src/galaxy/quikr.xml
@@ -11,23 +11,7 @@
 		<data name="output" format="tabular"/>
 	</outputs>
 	<help>
-**What it does**
-
-This tool counts the length of each fasta sequence in the file. The output file has two columns per line (separated by tab): fasta titles and lengths of the sequences. The option *How many characters to keep?* allows to select a specified number of letters from the beginning of each FASTA entry. 
-
------	
-
-**Example**
-
-Suppose you have the following FASTA formatted sequences from a Roche (454) FLX sequencing run::
-
-    &gt;EYKX4VC02EQLO5 length=108 xy=1826_0455 region=2 run=R_2007_11_07_16_15_57_
    TCCGCGCCGAGCATGCCCATCTTGGATTCCGGCGCGATGACCATCGCCCGCTCCACCACG
    TTCGGCCGGCCCTTCTCGTCGAGGAATGACACCAGCGCTTCGCCCACG
    &gt;EYKX4VC02D4GS2 length=60 xy=1573_3972 region=2 run=R_2007_11_07_16_15_57_
    AATAAAACTAAATCAGCAAAGACTGGCAAATACTCACAGGCTTATACAATACAAATGTAAfa
-
-Running this tool while setting **How many characters to keep?** to **14** will produce this::
-	
-	EYKX4VC02EQLO5  108
-	EYKX4VC02D4GS2	 60
-
-
 	</help>
 </tool>
+
+
diff --git a/src/galaxy/quikr_train.xml b/src/galaxy/quikr_train.xml
index b5f5291..a33d866 100644
--- a/src/galaxy/quikr_train.xml
+++ b/src/galaxy/quikr_train.xml
@@ -9,23 +9,5 @@
 		<data name="output" format="data"/>
 	</outputs>
 	<help>
-**What it does**
-
-This tool counts the length of each fasta sequence in the file. The output file has two columns per line (separated by tab): fasta titles and lengths of the sequences. The option *How many characters to keep?* allows to select a specified number of letters from the beginning of each FASTA entry. 
-
------	
-
-**Example**
-
-Suppose you have the following FASTA formatted sequences from a Roche (454) FLX sequencing run::
-
-    &gt;EYKX4VC02EQLO5 length=108 xy=1826_0455 region=2 run=R_2007_11_07_16_15_57_
    TCCGCGCCGAGCATGCCCATCTTGGATTCCGGCGCGATGACCATCGCCCGCTCCACCACG
    TTCGGCCGGCCCTTCTCGTCGAGGAATGACACCAGCGCTTCGCCCACG
    &gt;EYKX4VC02D4GS2 length=60 xy=1573_3972 region=2 run=R_2007_11_07_16_15_57_
    AATAAAACTAAATCAGCAAAGACTGGCAAATACTCACAGGCTTATACAATACAAATGTAAfa
-
-Running this tool while setting **How many characters to keep?** to **14** will produce this::
-	
-	EYKX4VC02EQLO5  108
-	EYKX4VC02D4GS2	 60
-
-
 	</help>
 </tool>
-- 
cgit v1.2.3