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Add --from_work_dir option in init_tool#276

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lecorguille:from_work_dir
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Add --from_work_dir option in init_tool#276
lecorguille wants to merge 1 commit intogalaxyproject:masterfrom
lecorguille:from_work_dir

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@lecorguille lecorguille commented Jul 31, 2015

The first part of my first contribution.

I just add an option --from_work_dir because we often succeed to avoid from_workr_dir argument.

Without --from_work_dir

    <command><![CDATA[
        samtools sort -o "$input1" > "$output1"
    ]]></command>
    <outputs>
        <data name="output1" format="bam" from_work_dir="1_sorted.bam" />
    </outputs>

With --from_work_dir

    <command><![CDATA[
        samtools sort -o "$input1" > "$output1"
    ]]></command>
    <outputs>
        <data name="output1" format="bam" />
    </outputs>

I hope I follow enough the good practice to not waste your time. Planemo, git and GitHub were almost new for me 2 days ago :)

Let me know if I was on the wrong way.

Gildas

jmchilton added a commit to jmchilton/planemo that referenced this pull request Jul 31, 2015
@jmchilton
Bugfix: tool_init use from_work_dir only if file in command.
07d0f78 
Fixes bug in the resulting tools using the output directly but having dummy from_work_dir files that are largely ignored by Galaxy under normal operation (but causing a somewhat more undefined behavior with Pulsar for instance). The updated example tools clarify this I think.

See also galaxyproject#276 (ping @lecorguille).
@jmchilton jmchilton mentioned this pull request Jul 31, 2015
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jmchilton commented Jul 31, 2015

Thanks for the contribution. That from_work_dir would be included and not used was a bug anyway. I think the following PR #277 fixes the bug and probably eliminates the need for your new flag. What do you think - is that an acceptable alternative?

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lecorguille commented Aug 3, 2015

More stylish ! Well done !
Thanks

@lecorguille lecorguille closed this Aug 3, 2015
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@lecorguille @jmchilton