comparison seqsero.xml @ 2:381e1e7109fc draft default tip

planemo upload commit 464b391afaa5819bc681452e85bea9d882730eb6-dirty

1:139f1e77d834

<tool id="seq_sero_reads_multiple" name="SeqSero Batch - Paired-End Reads" version="0.1.0">
	<description>Salmonella Serotype Prediction from Paired-End Reads</description>
        <command interpreter="python2.7">
                run_seqsero_batch_galaxy.py $input1 <!--$input2-->
                <!--test_bioblend.py $input1 $input2-->
        </command>
        <inputs>
                <param format="fastq,fastqsanger" name="input1" multiple="true" type="data" label="Source file"/>
                <!--<param format="fastq" name="input2" multiple="true" type="data" label="Source file"/>-->
        </inputs>
        <outputs>
                <data name="html_file" format="html" from_work_dir="Seqsero_result.html"/>
                <data name="text_file" format="txt" from_work_dir="Seqsero_result.txt"/>
        </outputs>
        <help>
               This tool predicts Salmonella serotypes from shotgun WGS data.

          	Below is the link to the seqsero help

               https://galaxy.ravencloudhpc.com/static/toolpages/seqsero/seqsero.html

                  Pages="1685--1692",
                  Month="May"
          }
          </citation>
     </citations>
        <stdio>
                <exit_code range="0:" level="warning"/>
                <regex match="Error:"/>
        </stdio>
</tool>

2:381e1e7109fc

<tool id="seq_sero_reads_multiple" name="SeqSero Batch - Paired-End Reads" version="0.1.0">
  <description>Salmonella Serotype Prediction from Paired-End Reads</description>  
<requirements>
	<requirement type="package" version="1.69">biopython</requirement>
        <requirement type="package" version="0.5.9">bwa</requirement>
        <requirement type="package" version="1.3.1">samtools</requirement>
        <requirement type="package" version="2.5.0">blast</requirement>
        <requirement type="package" version="2.6.2">sra_toolkit</requirement>
  </requirements>
       <stdio>
                <exit_code range="0:" level="warning"/>
                <regex match="Error:"/>
        </stdio>  
      <command interpreter="python2.7">
                run_seqsero_batch_galaxy.py $input1 <!--$input2-->
                <!--test_bioblend.py $input1 $input2-->
        </command>
        <inputs>
                <param format="fastq" name="input1" multiple="true" type="data" label="Source file"/>
                <!--<param format="fastq" name="input2" multiple="true" type="data" label="Source file"/>-->
        </inputs>
        <outputs>
                <data name="html_file" format="html" from_work_dir="Seqsero_result.html"/>
                <data name="text_file" format="txt" from_work_dir="Seqsero_result.txt"/>
        </outputs>
 	<tests>
        <test>
            <output  name="text_file" file="Seqsero_result.txt" ftype="txt"/>
 	</test>
    	</tests>
	<help>
               This tool predicts Salmonella serotypes from shotgun WGS data.

          	Below is the link to the seqsero help

               https://galaxy.ravencloudhpc.com/static/toolpages/seqsero/seqsero.html

                  Pages="1685--1692",
                  Month="May"
          }
          </citation>
     </citations>
</tool>