Mercurial > repos > matt-shirley > sra_tools

changeset 21:d850324e82cf draft

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fix datatype reference, increment versions
author Matt Shirley <mdshw5@gmail.com>
date Wed, 19 Jun 2013 13:31:58 -0400
parents a1255154fa3f
children 423f3eb06428
files fastq_dump.xml sam_dump.xml sra_fetch.xml
diffstat 3 files changed, 8 insertions(+), 10 deletions(-) [+]
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line diff
--- a/fastq_dump.xml	Mon Jun 17 21:41:27 2013 -0400
+++ b/fastq_dump.xml	Wed Jun 19 13:31:58 2013 -0400
@@ -1,9 +1,9 @@
-<tool id="fastq_dump" name="Extract fastq" version="1.0.1">
+<tool id="fastq_dump" name="Extract fastq" version="1.0.2">
   <description> format reads from NCBI SRA.</description>
   <command>fastq-dump --log-level fatal --accession '${input.name}' --stdout $split $aligned '$input' > $output </command>
   <version_string>fastq-dump --version</version_string>
   <inputs>
-    <param format="sra" name="input" type="data" label="sra archive"/>
+    <param format="SRA" name="input" type="data" label="sra archive"/>
     <param format="text" name="split" type="select" value="">
       <label>Split read pairs</label>
       <option value="">No</option>
--- a/sam_dump.xml	Mon Jun 17 21:41:27 2013 -0400
+++ b/sam_dump.xml	Wed Jun 19 13:31:58 2013 -0400
@@ -1,9 +1,9 @@
-<tool id="sam_dump" name="Extract SAM" version="1.0.1">
+<tool id="sam_dump" name="Extract SAM" version="1.0.2">
   <description> format reads from NCBI SRA.</description>
   <command>sam-dump $header $aligned $primary '$input' > $output</command>
   <version_string>sam-dump --version</version_string>
   <inputs>
-    <param format="sra" name="input" type="data" label="sra archive"/>
+    <param format="SRA" name="input" type="data" label="sra archive"/>
     <param format="text" name="header" type="select" value="">
       <label>Output SAM header</label>
       <option value="--header">Yes</option>
@@ -27,7 +27,8 @@
     <requirement type="package" version="2.3.2-4">sra_toolkit</requirement>
   </requirements>
   <help>
-    This tool extracts SAM format reads from SRA archives using sam-dump. The sam-dump program is developed at NCBI, and is available at: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software.
-Contact Matt Shirley at mdshw5@gmail.com for support and bug reports.
+    This tool extracts SAM format reads from SRA archives using sam-dump. 
+    The sam-dump program is developed at NCBI, and is available at: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software.
+    Contact Matt Shirley at mdshw5@gmail.com for support and bug reports.
   </help>
 </tool>
--- a/sra_fetch.xml	Mon Jun 17 21:41:27 2013 -0400
+++ b/sra_fetch.xml	Wed Jun 19 13:31:58 2013 -0400
@@ -1,4 +1,4 @@
-<tool id="sra_fetch" name="Fetch SRA" version="1.0.2">
+<tool id="sra_fetch" name="Fetch SRA" version="1.0.3">
   <description> by accession from NCBI SRA.</description>
   <command interpreter="python">sra_fetch.py --accession '$accession' --out '$output'</command>
   <inputs>
@@ -7,9 +7,6 @@
   <outputs>
     <data format="sra" name="output" label="Fetch ${accession.value}"/>
   </outputs>
-  <requirements>
-    <requirement type="python">sra_fetch.py</requirement>
-  </requirements>
   <help>
     This tool fetches SRA archives from NCBI over FTP using the python ftplib.
   </help>