Previous changeset 6:f396701fbf32 (2017-05-10) Next changeset 8:8cbc866b72ce (2021-04-16) |
Commit message:
v0.1.4 Internal changes to command line handling |
modified:
tools/fastq_paired_unpaired/README.rst tools/fastq_paired_unpaired/fastq_paired_unpaired.xml |
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diff -r f396701fbf32 -r 2709a0f065c9 tools/fastq_paired_unpaired/README.rst --- a/tools/fastq_paired_unpaired/README.rst Wed May 10 13:28:59 2017 -0400 +++ b/tools/fastq_paired_unpaired/README.rst Tue May 16 08:53:57 2017 -0400 |
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@@ -74,6 +74,8 @@ v0.1.3 - Minor internal changes to Python script for error reporting & style. - Updated to point at Biopython 1.67 (latest version in Tool Shed). - Explicit dependency on ``galaxy_sequence_utils``. +v0.1.4 - Use ``<command detect_errors="aggressive">`` (internal change only). + - Single quote command line arguments (internal change only). ======= ====================================================================== |
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diff -r f396701fbf32 -r 2709a0f065c9 tools/fastq_paired_unpaired/fastq_paired_unpaired.xml --- a/tools/fastq_paired_unpaired/fastq_paired_unpaired.xml Wed May 10 13:28:59 2017 -0400 +++ b/tools/fastq_paired_unpaired/fastq_paired_unpaired.xml Tue May 16 08:53:57 2017 -0400 |
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@@ -1,21 +1,18 @@ -<tool id="fastq_paired_unpaired" name="Divide FASTQ file into paired and unpaired reads" version="0.1.3"> +<tool id="fastq_paired_unpaired" name="Divide FASTQ file into paired and unpaired reads" version="0.1.4"> <description>using the read name suffices</description> <requirements> <requirement type="package" version="1.0.1">galaxy_sequence_utils</requirement> <requirement type="package" version="1.67">biopython</requirement> </requirements> - <stdio> - <!-- Anything other than zero is an error --> - <exit_code range="1:" /> - <exit_code range=":-1" /> - </stdio> - <version_command interpreter="python">fastq_paired_unpaired.py --version</version_command> - <command interpreter="python"> -fastq_paired_unpaired.py $input_fastq.extension $input_fastq + <version_command> +python $__tool_directory__/fastq_paired_unpaired.py --version + </version_command> + <command detect_errors="aggressive"> +python $__tool_directory__/fastq_paired_unpaired.py '$input_fastq.extension' '$input_fastq' #if $output_choice_cond.output_choice=="separate" - $output_forward $output_reverse + '$output_forward' '$output_reverse' #elif $output_choice_cond.output_choice=="interleaved" - $output_paired + '$output_paired' #end if $output_singles </command> |