Mercurial > repos > iuc > sra_tools

changeset 22:751a694ec620 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 1db2b3ee758847b8b63f58fb2075961003ff8c22"
author iuc
date Mon, 20 Jul 2020 07:27:41 -0400
parents 494b2ec08162
children 653e89d73fc4
files fasterq_dump.xml fastq_dump.xml sam_dump.xml sra_macros.xml
diffstat 4 files changed, 4 insertions(+), 4 deletions(-) [+]
line wrap: on
line diff
--- a/fasterq_dump.xml	Mon Jul 06 19:46:26 2020 -0400
+++ b/fasterq_dump.xml	Mon Jul 20 07:27:41 2020 -0400
@@ -1,4 +1,4 @@
-<tool id="fasterq_dump" name="Faster Download and Extract Reads in FASTQ" version="@VERSION@+galaxy1" profile="18.01">
+<tool id="fasterq_dump" name="Faster Download and Extract Reads in FASTQ" version="@VERSION@+galaxy2" profile="18.01">
     <description>format from NCBI SRA</description>
     <macros>
         <import>sra_macros.xml</import>
--- a/fastq_dump.xml	Mon Jul 06 19:46:26 2020 -0400
+++ b/fastq_dump.xml	Mon Jul 20 07:27:41 2020 -0400
@@ -1,4 +1,4 @@
-<tool id="fastq_dump" name="Download and Extract Reads in FASTA/Q" version="@VERSION@+galaxy1" profile="18.01">
+<tool id="fastq_dump" name="Download and Extract Reads in FASTA/Q" version="@VERSION@+galaxy2" profile="18.01">
     <description>format from NCBI SRA</description>
     <macros>
         <import>sra_macros.xml</import>
--- a/sam_dump.xml	Mon Jul 06 19:46:26 2020 -0400
+++ b/sam_dump.xml	Mon Jul 20 07:27:41 2020 -0400
@@ -1,4 +1,4 @@
-<tool id="sam_dump" name="Download and Extract Reads in BAM" version="@VERSION@+galaxy1" profile="18.01">
+<tool id="sam_dump" name="Download and Extract Reads in BAM" version="@VERSION@+galaxy2" profile="18.01">
     <description>format from NCBI SRA</description>
     <macros>
         <import>sra_macros.xml</import>
--- a/sra_macros.xml	Mon Jul 06 19:46:26 2020 -0400
+++ b/sra_macros.xml	Mon Jul 20 07:27:41 2020 -0400
@@ -23,7 +23,7 @@
                 #set $column = $input.file_list.unsanitized.metadata.column_names.index('Run') + 1
                 cut -f $column '$input.file_list'| tail -n +2 > "manifest" &&
             #else
-                ln -s '$input.file_list' > manifest &&
+                ln -s '$input.file_list' manifest &&
             #end if
             for acc in `@ACCESSIONS_FROM_FILE@ manifest` ;
             do (