planemo t: JobOutputsError occurs, but example_output and script outputs are the same

Question: planemo t: JobOutputsError occurs, but example_output and script outputs are the same

6 months ago by

South Korea

Hello,

planemo t is giving me JobOutputsError: History item different than expected, difference (using diff):, when the output from the md5sum results of the example_output and the script output are the same.

My XML put in planemo t:

<tool id="region_filter" name="Filter out variants not in the vicinity of refFlat genes" version="0.1.0">
    <requirements>
        <requirement type="package">python</requirement>
        <requirement type="package">pytabix</requirement>
    </requirements>
     "$output1"
    ]]>
    <inputs>
        <param type="data" name="input1" format="vcf"/>
        <param type="data" name="input2" format="gz"/>
    </inputs>
    <outputs>
        <data name="output1" format="vcf"/>
    </outputs>
    <tests>
        <test>
            <param name="input1" value="/dat1/github/rainbow/examples/test_snpEff.vcf"/>
            <param name="input2" value="/dat1/rgkorea/bam_files/rainbow/data/index/refFlat.bed.gz"/>
            
        </test>
    </tests>
    <help> <in.db.bed.gz>


    ]]></help>
    <citations>
        <citation type="bibtex">
@misc{githubrainbow,
  author = {LastTODO, FirstTODO},
  year = {TODO},
  title = {rainbow},
  publisher = {GitHub},
  journal = {GitHub repository},
  url = {https://github.com/alexbmp/rainbow},
}</citation>
    </citations>
</tool>

My planemo t region_filter.xml results (stdout and stderr file for planemo t: region_filter.log):

planemo t region_filter.xml > region_filter.log 2>&1
cat region_filter.log | grep JobOutputsError
JobOutputsError: History item  different than expected, difference (using diff):

But when I copy-paste the input1 and input2 of my XML and check the md5sum of the output, it's the same with the md5sum output of my example_output file:

md5sum /dat1/github/rainbow/examples/test_rflt.vcf
002cdccaf2d7fa4096d7bfd490196d19  /dat1/github/rainbow/examples/test_rflt.vcf
input1=/dat1/github/rainbow/examples/test_snpEff.vcf
input2=/dat1/rgkorea/bam_files/rainbow/data/index/refFlat.bed.gz
python /dat1/github/rainbow/scripts/dbflt_refflat.py $input1 $input2 | md5sum
[Thu May 17 11:59:46 2018] dbflt_refflat.py run initiated.
002cdccaf2d7fa4096d7bfd490196d19  -
planemo t region_filter.xml > region_filter.log 2>&1
cat region_filter.log | grep JobOutputsError
JobOutputsError: History item  different than expected, difference (using diff):

Could you please give me some ideas about this?
Many thanks!

planemo planemo t galaxy test • 217 views

ADD COMMENT • link •

written 6 months ago by Seongmin Choi • 20

Similar posts • Search »