| Previous changeset 22:751a694ec620 (2020-07-20) Next changeset 24:e08a7ad4378b (2021-02-01) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 3c5c7587a9e8f4177db5ff1390b7e29cb190eb72" |
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modified:
fasterq_dump.xml fastq_dump.xml sam_dump.xml sra_macros.xml |
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| diff -r 751a694ec620 -r 653e89d73fc4 fasterq_dump.xml --- a/fasterq_dump.xml Mon Jul 20 07:27:41 2020 -0400 +++ b/fasterq_dump.xml Thu Aug 20 05:06:27 2020 -0400 |
| [ |
| @@ -1,4 +1,4 @@ -<tool id="fasterq_dump" name="Faster Download and Extract Reads in FASTQ" version="@VERSION@+galaxy2" profile="18.01"> +<tool id="fasterq_dump" name="Faster Download and Extract Reads in FASTQ" version="@VERSION@+galaxy0" profile="18.01"> <description>format from NCBI SRA</description> <macros> <import>sra_macros.xml</import> @@ -6,6 +6,7 @@ <expand macro="requirements"/> <version_command>fasterq-dump --version</version_command> <command detect_errors="exit_code"><![CDATA[ + set -o | grep -q pipefail && set -o pipefail; @COPY_CONFIGFILE@ @SET_ACCESSIONS@ #if $input.input_select == "file": @@ -19,7 +20,7 @@ #if str( $adv.minlen ) != "": --min-read-len "$adv.minlen" #end if - $adv.skip_technical >> $log 2>&1 ; + $adv.skip_technical 2>&1 | tee $log; if [ \$? == 0 ] && [ \$(ls *.fastq | wc -l) -ge 1 ]; then break ; else |
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| diff -r 751a694ec620 -r 653e89d73fc4 fastq_dump.xml --- a/fastq_dump.xml Mon Jul 20 07:27:41 2020 -0400 +++ b/fastq_dump.xml Thu Aug 20 05:06:27 2020 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="fastq_dump" name="Download and Extract Reads in FASTA/Q" version="@VERSION@+galaxy2" profile="18.01"> +<tool id="fastq_dump" name="Download and Extract Reads in FASTA/Q" version="@VERSION@+galaxy0" profile="18.01"> <description>format from NCBI SRA</description> <macros> <import>sra_macros.xml</import> |
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| diff -r 751a694ec620 -r 653e89d73fc4 sam_dump.xml --- a/sam_dump.xml Mon Jul 20 07:27:41 2020 -0400 +++ b/sam_dump.xml Thu Aug 20 05:06:27 2020 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="sam_dump" name="Download and Extract Reads in BAM" version="@VERSION@+galaxy2" profile="18.01"> +<tool id="sam_dump" name="Download and Extract Reads in BAM" version="@VERSION@+galaxy0" profile="18.01"> <description>format from NCBI SRA</description> <macros> <import>sra_macros.xml</import> |
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| diff -r 751a694ec620 -r 653e89d73fc4 sra_macros.xml --- a/sra_macros.xml Mon Jul 20 07:27:41 2020 -0400 +++ b/sra_macros.xml Thu Aug 20 05:06:27 2020 -0400 |
| [ |
| @@ -1,5 +1,5 @@ <macros> - <token name="@VERSION@">2.10.7</token> + <token name="@VERSION@">2.10.8</token> <token name="@ACCESSIONS_FROM_FILE@"> grep '^[[:space:]]*[E|S|D]RR[0-9]\{1,\}[[:space:]]*$' </token> |