comparison ectyper.xml @ 4:08d801182fa1 draft default tip

"planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 6615f6e5ae2eac1f8e90f25e1707c8b7ab161517"

3:fb3683870b74

<tool id="ectyper" name="ectyper" version="0.9.1">
  <description>ectyper is a standalone serotyping module for Escherichia coli. It supports fasta and fastq file formats.</description>
  <requirements>
     <requirement type="package" version="0.9.1">ectyper</requirement>
  </requirements>
  <command detect_errors="exit_code">
  <![CDATA[
  #set $genomes = ''
  #if hasattr($input, '__iter__')

  #else
    ln -s "${input}" "${input.element_identifier}" &&
    #set $genomes = $input.element_identifier
  #end if

  #if $mash_input
    ln -s "${mash_input}" mash_sketch.msh &&
  #end if

  ectyper  --cores \${GALAXY_SLOTS:-4} 
  --input "${genomes}" 
  --percentIdentity '$adv_param.min_percentIdentity'
  --percentLength '$adv_param.percentLength'
  #if $adv_param.verifyEcoli
    --verify
  #end if
  #if $mash_input
    --refseq mash_sketch.msh
  #end if   
  #if $adv_param.alleleSequence
    --sequence
  #end if
  --output '.'
  ]]>
  </command>
  <inputs>
    <param name="input" type="data"  format="fastq,fasta" label="Genome(s) input(s)" help="FASTA or FASTQ file(s)"/>
    <param name="mash_input" type="data" optional="true" format="binary" label="Mash genome sketches (Optional)" help="Optionally provide custom MASH genome sketch to help with species identification (otherwise default RefSeq sketch is used)"/>
    <section name="adv_param" title="Advanced parameters" expanded="False">
      <param name="min_percentIdentity" type="integer" value="90" min="1" max="100"/>
      <param name="percentLength" type="integer" value="10" min="1" max="100"/>
      <param name="verifyEcoli" type="boolean" checked="true" label="Enable E. coli species verification"/>
      <param name="alleleSequence" type="boolean" checked="false" label="Print the allele sequences as the final columns of the output?"/> 
      <param name="logging" type="boolean" checked="false"  label="Include log file in the run outputs?" />
    </section>  
  </inputs>
  <outputs>
    <data name="output_result" format="tabular" from_work_dir="output.tsv" label="${tool.name} serotype report on ${input.element_identifier}"> </data>
    <data name="output_log" format="txt" from_work_dir="ectyper.log" label="${tool.name} log file on ${input.element_identifier}">
        <filter>adv_param['logging']==True</filter>
    </data>   
  </outputs>
  <tests>
    <test>
      <param name="input" value="Escherichia2.fastq"/>
      <assert_stderr>

  <help>
**Syntax**


This tool identifies the serotype of assembled or assembly-free Escherichia coli genome sample based on a set of either *wzm/wzt* or *wzx/wzy* and *fliC/flkA/flmA* alleles corresponding to O and H antigens, respectively.
The non-E.coli genomes and other Escherichia genus species are successfully identified and well handled. The 0.9.0 version improves tool sensitivy when target alleles are truncated or
poorly covered by raw reads.


For more information please visit https://github.com/phac-nml/ecoli_serotyping. 

-----

**Input:**

Accepts a variety of inputs including both single and/or multiple FASTQ and/or FASTA file(s). Inputs might contain pure raw reads, but for more accurate results, draft assemblies are recommended.

The default MASH RefSeq genome sketch is included and updated every 6 months, but one can supply custom sketch file for species identification.

One can download RefSeq genome sketch containing approximately 91,283 genomes from https://gembox.cbcb.umd.edu/mash/refseq.genomes.k21s1000.msh.


**Output:**

Tab-delimited report listing identified O and H antigens together with corresponding highest scoring alleles and normalized BLAST score defined as (%identity x query coverage length) / 10000

-----

**Parameters (Optional):**

  - **Print the allele sequences as the final columns of the output?** Turn ON/OFF addition of the actual O and H antigen allelic sequences in the report
  - **Enable E. coli species verification:** Turn ON/OFF for more rigorous species verification (recommended)
  - **Include log file in the run outputs?:** Turn ON/OFF optional output of the ectyper log file for a more detailed results assessment

  </help>
<citations>
    <citation type="bibtex">
  @misc{githubectyper,

4:08d801182fa1

<tool id="ectyper" name="ectyper" version="1.0.0">
  <description>ectyper is a standalone serotyping module for Escherichia coli. It supports fasta and fastq file formats.</description>
  <requirements>
     <requirement type="package" version="1.0.0">ectyper</requirement>
  </requirements>
  <command detect_errors="exit_code">
  <![CDATA[
  #set $genomes = ''
  #if hasattr($input, '__iter__')

  #else
    ln -s "${input}" "${input.element_identifier}" &&
    #set $genomes = $input.element_identifier
  #end if

  #if $adv_param.mash_input
    ln -s "${adv_param.mash_input}" mash_sketch.msh &&
  #end if


  #if $adv_param.db_input
    ln -s "${adv_param.db_input}" custom_db.json &&
  #end if


  ectyper  --cores \${GALAXY_SLOTS:-4} 
  --input "${genomes}" 
  -opid '$adv_param.opid'
  -opcov '$adv_param.opcov'
  -hpid '$adv_param.hpid'
  -hpcov '$adv_param.hpcov'

  #if $adv_param.verifyEcoli
    --verify
  #end if

  #if $adv_param.mash_input
    --refseq mash_sketch.msh
  #end if

  #if $adv_param.db_input
    --dbpath custom_db.json
  #end if

  --output '.'
  ]]>
  </command>
  <inputs>
    <param name="input" type="data"  format="fastq,fasta" label="Genome(s) input(s)" help="FASTA or FASTQ file(s)"/>
    <section name="adv_param" title="Advanced parameters" expanded="False">
      <param name="opid" label="O antigen minimum %identity" type="integer" value="90" min="1" max="100"/>
      <param name="opcov" label="O antigen minimum %coverage" type="integer" value="90" min="1" max="100"/>
      <param name="hpid" label="H antigen minimum %identity" type="integer" value="95" min="1" max="100"/>
      <param name="hpcov" label="H antigen minimum %coverage" type="integer" value="50" min="1" max="100"/>
      <param name="verifyEcoli" type="boolean" checked="true" label="Enable E. coli species verification"/>
      <param name="blastresults" type="boolean" checked="false"  label="Include BLAST allele alignment results tab-delim file in the outputs?" />
      <param name="logging" type="boolean" checked="false"  label="Include log file in the run outputs?" />
      <param name="mash_input" type="data" optional="true" format="binary" label="Mash genome sketches (Optional)" help="Optionally provide custom MASH genome sketch to help with species identification (otherwise default RefSeq sketch is used)"/>
      <param name="db_input" type="data" optional="true" format="json" label="Custom database of alleles (Optional)" help="Optionally provide custom database of alleles in JSON format"/>
    </section>
  </inputs>
  <outputs>
    <data name="output_result" format="tabular" from_work_dir="output.tsv" label="${tool.name} serotype report on ${input.element_identifier}"> </data>
    <data name="output_log" format="txt" from_work_dir="ectyper.log" label="${tool.name} log file on ${input.element_identifier}">
        <filter>adv_param['logging']==True</filter>
    </data>
    <data name="output_blast" format="tabular" from_work_dir="blast_output_alleles.txt"  label="${tool.name} BLAST results file on ${input.element_identifier}">
         <filter>adv_param['blastresults']==True</filter>
    </data>
  </outputs>
  <tests>
    <test>
      <param name="input" value="Escherichia2.fastq"/>
      <assert_stderr>

  <help>
**Syntax**


This tool identifies the serotype of both assembled or assembly-free Escherichia coli genome samples based on a set of the key O and H antigen determinant genes including *wzm/wzt* or *wzx/wzy* and *fliC/flkA/flmA*.
Unique to the tool, species identification module allows for non-E.coli genomes identification including other Escherichia genus species.
This version improves antigen call rates on "difficult samples" by use of an adaptive threshold. This is especially useful when antigen genes are truncated or poorly covered by raw reads.
If no antigen call is being predicted by the tool, try to lower %coverage parameter first. For more information on the new Quality Control module and running parameter details please visit https://github.com/phac-nml/ecoli_serotyping.


-----

**Input:**

Accepts a variety of inputs including both single and/or multiple FASTQ and/or FASTA file(s). Inputs might contain pure raw reads, but for more accurate results, draft assemblies are recommended.


The default MASH RefSeq genome sketch (https://gembox.cbcb.umd.edu/mash/refseq.genomes.k21s1000.msh) containing approximately 91K genomes is included and automatically updated every 6 months.



**Output:**

Tab-delimited report listing identified O and H antigens together with corresponding the highest-scoring alleles and normalized BLAST score defined as (%identity x %coverage) / 1e4.
If *verifyEcoli* parameter is enabled, final report will contain allele quality control information on results for reporting purposes. PASS (REPORTABLE) QC flag means that O and H antigen calls are of sufficient to unambiguously resolve them from all other antigens.

-----

**Parameters (Optional):**
  - **Enable E. coli species verification:** for species verification in case samples are of non-E.coli origin
  - **Include BLAST allele alignment results tab-delim file in the outputs?** Get reference allele sequences and detailed BLAST output
  - **Include log file in the run outputs?:** Get optional logs of the ectyper run for a more detailed results assessment and troubleshooting

  </help>
<citations>
    <citation type="bibtex">
  @misc{githubectyper,