Question: adding some tools into galaxy using xml
0
gravatar for cagalli
3.4 years ago by
cagalli30
Germany
cagalli30 wrote:

HEY guys,
I have got some problems.I want to add a tool into galaxy.But following the xml below,what I get is always tac $input.
It cannot distinguish -b,-r.And I also do not know how to make -s string run in it.So I would like you to recommand me some materials to read,and figure out how it works.

<tool id="tac1" name="tac datasets">
    <description>tail-to-head</description>
    <command>
    <![CDATA[
        tac
        -b
        -r        
        $input1
        > $out_file1
        
        ]]>
        
    </command>
    <inputs>
        <param name="input1" type="data" label="Tac Dataset"/>
        <param name="delimiter" type="select" label="Delimited by">
      <option value="N">Null</option>
      <option value="B">-b</option>
      <option value="R">-r</option>
      <option value="S">-s</option>
    </param>
    </inputs>
    <outputs>          

        <data name="out_file1" format="input" metadata_source="input1"/>

    </outputs>
    <tests>
        <test>
            <param name="delimiter" value="N"/>    
            <param name="input1" value="1.bed"/>
            <output name="out_file1" file="tac_wrapper_out1.bed"/>
        </test>
        <!--TODO: if possible, enhance the underlying test code to handle this test
            the problem is multiple params with the same name "input2"
        <test>
            <param name="input1" value="1.bed"/>
            <param name="input2" value="2.bed"/>
            <param name="input2" value="3.bed"/>
            <output name="out_file1" file="cat_wrapper_out2.bed"/>
        </test>
        -->
    </tests>

</tool>

 

shell command galaxy xml • 1.2k views
ADD COMMENTlink modified 3.4 years ago by Bjoern Gruening5.0k • written 3.4 years ago by cagalli30
0
gravatar for cagalli
3.4 years ago by
cagalli30
Germany
cagalli30 wrote:

Or I mean,if I want to use bash command in XML file.What kind of -s can I write into?

  <command>
    <![CDATA[
        tac
        -b
        -r  
        -s $seperator1
        "$seperator1"

        $input1
        > $out_file1
        
        ]]>
        
    </command>

If I add -s,it never works.But without it,it somehow works.

ADD COMMENTlink written 3.4 years ago by cagalli30
0
gravatar for Bjoern Gruening
3.4 years ago by
Bjoern Gruening5.0k
Germany
Bjoern Gruening5.0k wrote:

This was solved off the list ...

ADD COMMENTlink written 3.4 years ago by Bjoern Gruening5.0k
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