Hi, I'm new to publishing tools/repository on the toolshed. I have used
planemo and lint and tests as well as serve all worked. I was able to use
the tool. However, when I uploaded it onto the test tool shed and imported
the tool on a cloud instance, I keep getting this error when running job:
Fatal error: Exit code 2 () Can't open perl script
"rm_consecutive_sameScore.pl": No such file or directory
Please advise! I've been downloading and looking at what others did but I
still can't figure this out.
I've attached my .xml file and here are some of the commands I used to
upload the tool.
planemo shed_create --shed_target testtoolshed
<tool id="jose123" name="removes_consecutive_same_scored_bins" version="0.1.0">
<requirements>
</requirements>
<stdio>
<exit_code range="1:" />
</stdio>
<command interpreter="perl">.$__tool_directory__/rm_consecutive_sameScore.pl "$input1" "$output1"
</command>
<inputs>
<param type="data" name="input1" format="bed" />
</inputs>
<outputs>
<data name="output1" format="bed" />
</outputs>
<tests>
<test>
<param name="input1" value="LmnB1_chip_256-big_chr19.bed"/>
<output name="output1" file="output.bed"/>
</test>
</tests>
<help><![CDATA[
Usage: Removes consecutive bins (> n) with same scores
]]></help>
<citations>
<citation type="bibtex">
@misc{renameTODO,
author = {LastTODO, FirstTODO},
year = {TODO},
title = {TODO},
url = {manuscript in preparation},
}</citation>
</citations>
</tool>
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