Previous changeset 9:6c60903f70ac (2017-07-12) Next changeset 11:5e6237d58b0c (2018-05-16) |
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 48c9d7f30655d48c9b46b9ca7a17c454eb54694d |
modified:
sam_dump.xml |
b |
diff -r 6c60903f70ac -r 8c00bc7fd8de sam_dump.xml --- a/sam_dump.xml Wed Jul 12 00:48:56 2017 -0400 +++ b/sam_dump.xml Fri Nov 17 13:22:37 2017 -0500 |
[ |
@@ -1,4 +1,4 @@ -<tool id="sam_dump" name="Download and Extract Reads in BAM" version="@VERSION@.2"> +<tool id="sam_dump" name="Download and Extract Reads in BAM" version="@VERSION@.3"> <description>format from NCBI SRA</description> <macros> <import>sra_macros.xml</import> @@ -6,7 +6,7 @@ <expand macro="requirements"/> <version_command>sam-dump --version</version_command> <command detect_errors="exit_code"> - <![CDATA[ +<![CDATA[ #if $input.input_select=="file_list": for acc in `cat $input.file_list` ; do @@ -18,8 +18,6 @@ [ ""\$acc" =~ ^[E|S|D]RR[0-9]{1,}$" ] && ( #end if - - ## Need to set the home directory to the current working directory, ## else the tool tries to write to home/.ncbi and fails when used ## with a cluster manager. @@ -38,19 +36,15 @@ #end if sam-dump --log-level fatal --disable-multithreading #if str( $adv.region ) != "": - --aligned-region "$adv.region" + --aligned-region '$adv.region' #end if #if str( $adv.matepairDist ) != "": - --matepair-distance "$adv.matepairDist" + --matepair-distance '$adv.matepairDist' #end if #if str( $adv.minMapq ) != "": - --min-mapq "$adv.minMapq" + --min-mapq '$adv.minMapq' #end if - #if str( $adv.header ) == "yes": - --header - #else: - --no-header - #end if + --header #if str( $adv.alignments ) == "both": --unaligned #end if @@ -61,7 +55,7 @@ --primary #end if #if $input.input_select == "file": - "$input.file" + '$input.file' #elif $input.input_select == "accession_number": "\$acc" #elif $input.input_select=="file_list": @@ -72,9 +66,9 @@ | samtools view -Sb - 2> /dev/null #end if #if $input.input_select == "file": - > "$output_file" + > '$output_file' #elif $input.input_select == "accession_number": - > "$output_accession" ) + > '$output_accession' ) #end if #if $input.input_select=="file_list": @@ -86,7 +80,6 @@ ) ; done #end if - ]]> </command> <inputs> @@ -96,11 +89,6 @@ <option value="sam">sam</option> </param> <section name="adv" title="Advanced Options" expanded="False"> - <param name="header" type="select" value="yes"> - <label>output header</label> - <option value="yes">Yes</option> - <option value="no">No</option> - </param> <expand macro="alignments"/> <expand macro="region"/> <expand macro="matepairDist"/> @@ -141,6 +129,7 @@ </test> </tests> <help><![CDATA[ + **What it does?** This tool extracts data (in BAM_ format) from the Short Read Archive (SRA) at the National Center for Biotechnology Information (NCBI). It is based on the sam-dump_ utility of the SRA Toolkit. @@ -191,7 +180,6 @@ .. _collection: https://galaxyproject.org/tutorials/collections/ .. _link: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies - @SRATOOLS_ATTRRIBUTION@ ]]></help> <expand macro="citation"/> |