Question: add custom tools to local galaxy
0
gravatar for chenzhuod
5 weeks ago by
chenzhuod0
chenzhuod0 wrote:

hi,

I'm installing tools to galaxy, but some tools are not existed in tool shed, such as fqtrim. So, I install them by the method according to https://galaxyproject.org/admin/tools/add-tool-tutorial/.

But, it can not be found in my galaxy, I think the problem is xml file.

<tool id="fqtrim" name="fqtrim-0.9.7" version="0.9.7">
  <description>can be used as a pre-processing or filtering step for next-generation sequence analysis pipelines (e.g. mapping, assembly) or as a post-processing utility for the analysis and potential recovery of unmapped reads or singletons resulting from such a pipeline</description>

  <command><![CDATA[

fqtrim

## Minimum length of reads to be kept
-l \${min_length_kept} 

## trim polyA/T at both ends
-B

## use <numcpus> CPUs (threads) on the local machine
-p \${GALAXY_SLOTS:-1}

   -o trim.fq

   '${read1}','${read2}'

  ]]></command>


   <inputs>
     <param name="min_length" argument="-l" type="integer" optional="true" label="Minimum length of reads to be kept">
     <param name="threads" argument="-p" type="integer" optional="true" label="use CPUs (threads) on the local machine">
   </inputs>

  <outputs>
    <data name="trim.fq" label="${tool.name} on ${readtype.fastq_r1_in.name} (R1 paired)" format_source="fastq_r1_in">
      <filter>readtype['single_or_paired'] == "pair_of_files"</filter>
    </data>
    <data name="trim.fq" label="${tool.name} on ${readtype.fastq_r2_in.name} (R2 paired)" format_source="fastq_r2_in">
      <filter>readtype['single_or_paired'] == "pair_of_files"</filter>
    </data>
    </collection>
  </outputs>

</tool>

Is there any trouble?

Thanks!

ADD COMMENTlink modified 5 weeks ago by Jennifer Hillman Jackson24k • written 5 weeks ago by chenzhuod0
0
gravatar for Jennifer Hillman Jackson
5 weeks ago by
United States
Jennifer Hillman Jackson24k wrote:

Hello,

Are you using Planemo for tool development (or for modifying an existing tool)? If not yet, it is strongly recommended.

An overview of admin configuration is also in our docs.

Please see:

Thanks, Jen, Galaxy team

ADD COMMENTlink written 5 weeks ago by Jennifer Hillman Jackson24k

Thanks,

I've revised the xml file.

Another question. When fqtrim is running, galaxy could create a tmp file. In the bash file of the tmp file, directory of utput file could be added automatically. How can I control it? I mean, I don't need the directory of output file.

Chen Siyuan

ADD REPLYlink written 26 days ago by chenzhuod0
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