comparison sistr_cmd.xml @ 4:17fcac7ddf54 draft

"planemo upload commit 5d0cc76371b061089f1399d21aea86540cbcab4f"

3:5c8ff92e38a9

<tool id="sistr_cmd" name="sistr_cmd" version="1.0.2">
  <description>
    Salmonella In Silico Typing Resource commandline tool for serovar prediction
  </description>
  <requirements>
    <requirement type="package" version="1.0.2">sistr_cmd</requirement>
  </requirements>
  <stdio>
    <exit_code range="1:" />
  </stdio>
  <command><![CDATA[

      format="json"
      label="cgMLST allele match results" />
  </outputs>
  <tests>
    <test>
      <param name="input_fastas" value="AE014613-699860.fasta"/>
      <param name="output_format" value="tab"/>
      <output 
        name="cgmlst_profiles" 
        value="cgmlst-profiles.csv"
        ftype="csv"
        lines_diff="2">
        <assert_contents>
          <has_text text=",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,3969539340,2545200385,225275747,2955003506,2353669245,2666669453,1672513023,3779563470,1301843222,2161147266,607954140,3680021500,2914087704,1062106200,3673111880,1314942441,1367997025,3293595301,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,1528212814,2110459436,4160823845,1648892875,2084418558,1638162324,469721942,1317894045,1973458150,926214622,2197498164,398274060,,,,,,,,,,1154766063,278162969,490843778,3950769715,,,,,,4203409135,2061008354,,,,,,,1052128508,,,1510445340,,,4065472468,,,,,,1495737522,,,,,,,,3076491138,712233770,3105746335,625241463,3016847250,1928860657,2229984332,1341416065,2978539204,1175502179,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,1328452594,2372254687,2640609716,3051501604,3258707132,,,,,,,,,,,,1007978530,,3646345463,1109678443,,,,,,,,,"/>
        </assert_contents>
      </output>
      <output 
        name="output_prediction_tab" 
        value="sistr-results.tab"
        ftype="tabular"
        lines_diff="2">
        <assert_contents>
          <has_text text="AE014613-699860" />
          <has_text text="Typhi" />
          <has_text text="enterica" />
          <has_text text="-:-:-" />
          <has_n_columns n="21" />
        </assert_contents>
      </output>
      <output 
        name="alleles_output" 
        value="alleles-output.json"
        ftype="json"
        compare="sim_size"/>
    </test>
    <test>
      <param name="input_fastas" value="13-1101-Paratyphi_B.fasta"/>
      <param name="output_format" value="tab"/>
      <output 
        name="novel_alleles" 
        value="novel-alleles-13-1101.fasta"
        ftype="fasta"
        compare="sim_size"/>
      <output 
        name="cgmlst_profiles" 
        value="cgmlst-profiles-13-1101.csv"
        ftype="csv"
        lines_diff="2">
      </output>
      <output 
        name="output_prediction_tab" 
        value="sistr-results-13-1101.tab"
        ftype="tabular"
        lines_diff="2">
        <assert_contents>
          <has_text text="13-1101-Paratyphi_B" />
          <has_text text="Paratyphi B var. Java" />
          <has_text text="enterica" />
          <has_text text="1,4,[5],12" />
          <has_text text="PASS" />
          <has_n_columns n="21" />
        </assert_contents>
      </output>
      <output 
        name="alleles_output" 
        value="alleles-output-13-1101.json"
        ftype="json"
        compare="sim_size"/>
    </test>
    <test>
      <param name="input_fastas" value="13-1101 Paratyphi_B.fasta"/>
      <param name="output_format" value="tab"/>
      <output 
        name="novel_alleles" 
        value="novel-alleles-13-1101.fasta"
        ftype="fasta"
        compare="sim_size"/>
      <output 
        name="cgmlst_profiles" 
        value="cgmlst-profiles-13-1101.csv"
        ftype="csv"
        lines_diff="2">
      </output>
      <output 
        name="output_prediction_tab" 
        value="sistr-results-13-1101.tab"
        ftype="tabular"
        lines_diff="2">
        <assert_contents>
          <has_text text="13-1101 Paratyphi_B" />
          <has_text text="Paratyphi B var. Java" />
          <has_text text="enterica" />
          <has_text text="1,4,[5],12" />
          <has_text text="PASS" />
          <has_n_columns n="21" />
        </assert_contents>
      </output>
      <output 
        name="alleles_output" 
        value="alleles-output-13-1101.json"
        ftype="json"
        compare="sim_size"/>
    </test>
    <test>
      <param name="input_fastas" value="13-1101-Paratyphi_B.fasta"/>
      <param name="output_format" value="json"/>
      <param name="more_output" value="-MM"/>
      <output 
        name="output_prediction_json" 
        value="sistr-results-13-1101.json"
        ftype="json"
        compare="sim_size">
        <assert_contents>
          <has_text text="13-1101-Paratyphi_B" />
          <has_text text="Paratyphi B var. Java" />
          <has_text text="enterica" />
          <has_text text="1,4,[5],12" />
          <has_text text="PASS" />
        </assert_contents>
      </output>
    </test>
  </tests>
  <help>
  <![CDATA[

4:17fcac7ddf54

<tool id="sistr_cmd" name="sistr_cmd" version="@VERSION@">
  <description>
    Salmonella In Silico Typing Resource commandline tool for serovar prediction 
  </description>
  <macros>
     <token name="@VERSION@">1.1.1</token>
  </macros>
  <requirements>
    <requirement type="package" version="@VERSION@">sistr_cmd</requirement>
  </requirements>
  <stdio>
    <exit_code range="1:" />
  </stdio>
  <command><![CDATA[

      format="json"
      label="cgMLST allele match results" />
  </outputs>
  <tests>
    <test>
      <param name="input_fastas" value="AE014613-699860.fasta" ftype="fasta"/>
      <param name="output_format" value="tab"/>
      <output 
        name="cgmlst_profiles" 
        value="cgmlst-profiles.csv"
        ftype="csv"
        compare="diff">
      </output>
      <output name="output_prediction_tab" 
        ftype="tabular"
        value="sistr-results.tabular"
        compare="sim_size">
        <assert_contents>
          <has_text text="AE014613-699860" />
          <has_text text="Typhi" />
          <has_text text="enterica" />
          <has_text_matching expression="FAIL\t-\t-:-:-\t-:-:-"/>
          <has_text text="2014-LET-0419"/>
          <has_n_columns n="22" />
        </assert_contents>
      </output>
      <output 
        name="alleles_output" 
        value="alleles-output.json"
        ftype="json"
        compare="sim_size">
        <assert_contents>
          <has_text text="NZ_AOXE01000059.1"/>
          <has_text text="Salmonella enterica subsp. enterica serovar Typhi Ty2"/>
          <has_text text="NZ_AOXE01000033.1"/>
          <has_text text="NZ_AOXE01000052.1"/>  
        </assert_contents> 
      </output>
    </test>
    <test>
      <param name="input_fastas" value="13-1101-Paratyphi_B.fasta" ftype="fasta"/>
      <param name="output_format" value="tab"/>
      <output 
        name="novel_alleles" 
        value="novel-alleles-13-1101.fasta"
        ftype="fasta"
        compare="sim_size"/>
      <output 
        name="cgmlst_profiles" 
        value="cgmlst-profiles-13-1101.csv"
        ftype="csv"
        compare="diff">
      </output>
      <output 
        name="output_prediction_tab" 
        value="sistr-results-13-1101.tabular"
        ftype="tabular"
        compare="sim_size">
        <assert_contents>
          <has_text text="13-1101-Paratyphi_B"/>
          <has_text text="Paratyphi B var. Java"/>
          <has_text text="enterica"/>
          <has_text text="1,4,[5],12"/>
          <has_text text="PASS"/>
          <has_n_columns n="22"/>
        </assert_contents>
      </output>
      <output 
        name="alleles_output" 
        value="alleles-output-13-1101.json"
        ftype="json"
        compare="sim_size">
        <assert_contents>
          <has_text text="13-1101-Paratyphi_B"/>
          <has_text text="NZ_AOXE01000059.1"/>
        </assert_contents>
      </output> 
    </test>
  </tests>
  <help>
  <![CDATA[