attributor-prok-cheetah.cwl

#!/usr/bin/env cwl-runner

cwlVersion: v1.0
class: CommandLineTool
baseCommand: attributor

requirements:
- class: InlineJavascriptRequirement
- class: InitialWorkDirRequirement
  listing:
  - entry: |
      general:
         default_product_name: hypothetical protein
         allow_attributes_from_multiple_sources: No
         debugging_polypeptide_limit: 0
      indexes:
         coding_hmm_lib: $(inputs.hmm_attribute_lookup_file.path)
         uniref100: $(inputs.blast_attribute_lookup_file.path)
      input:
         polypeptide_fasta: $(inputs.polypeptide_fasta.path)
         gff3: $(inputs.source_gff3.path)
      order:
         - coding_hmm_lib__equivalog
         - rapsearch2__trusted_full_full
         - coding_hmm_lib__equivalog_domain
         - rapsearch2__trusted_partial_full
         - coding_hmm_lib__subfamily
         - coding_hmm_lib__superfamily
         - coding_hmm_lib__subfamily_domain
         - coding_hmm_lib__domain
         - coding_hmm_lib__pfam
         - rapsearch2__trusted_full_partial
         - rapsearch2__all_full_full
         - tmhmm
         #- lipoprotein_motif
         - coding_hmm_lib__hypothetical_equivalog
      evidence:
         - label: coding_hmm_lib__equivalog
           type: HMMer3_htab
           path: ${
             var r = "";
             for (var i = 0; i < inputs.hmm_files.length; i++) {
               if (i > 0) {
                 r += ",";
               }
               r += inputs.hmm_files[i].path.replace('file://','');
             }
             return r;
           }
           class: equivalog
           index: coding_hmm_lib

         - label: coding_hmm_lib__equivalog_domain
           type: HMMer3_htab
           path: ${
             var r = "";
             for (var i = 0; i < inputs.hmm_files.length; i++) {
               if (i > 0) {
                 r += ",";
               }
               r += inputs.hmm_files[i].path.replace('file://','');
             }
             return r;
           }
           class: equivalog_domain
           index: coding_hmm_lib

         - label: coding_hmm_lib__subfamily
           type: HMMer3_htab
           path: ${
             var r = "";
             for (var i = 0; i < inputs.hmm_files.length; i++) {
               if (i > 0) {
                 r += ",";
               }
               r += inputs.hmm_files[i].path.replace('file://','');
             }
             return r;
           }
           class: subfamily
           index: coding_hmm_lib
           append_text: family protein

         - label: coding_hmm_lib__superfamily
           type: HMMer3_htab
           path: ${
             var r = "";
             for (var i = 0; i < inputs.hmm_files.length; i++) {
               if (i > 0) {
                 r += ",";
               }
               r += inputs.hmm_files[i].path.replace('file://','');
             }
             return r;
           }
           class: superfamily
           index: coding_hmm_lib
           append_text: family protein

         - label: coding_hmm_lib__subfamily_domain
           type: HMMer3_htab
           path: ${
             var r = "";
             for (var i = 0; i < inputs.hmm_files.length; i++) {
               if (i > 0) {
                 r += ",";
               }
               r += inputs.hmm_files[i].path.replace('file://','');
             }
             return r;
           }
           class: subfamily_domain
           index: coding_hmm_lib
           append_text: domain protein

         - label: coding_hmm_lib__domain
           type: HMMer3_htab
           path: ${
             var r = "";
             for (var i = 0; i < inputs.hmm_files.length; i++) {
               if (i > 0) {
                 r += ",";
               }
               r += inputs.hmm_files[i].path.replace('file://','');
             }
             return r;
           }
           class: domain
           index: coding_hmm_lib
           append_text: domain protein

         - label: coding_hmm_lib__pfam
           type: HMMer3_htab
           path: ${
             var r = "";
             for (var i = 0; i < inputs.hmm_files.length; i++) {
               if (i > 0) {
                 r += ",";
               }
               r += inputs.hmm_files[i].path.replace('file://','');
             }
             return r;
           }
           class: pfam
           index: coding_hmm_lib
           append_text: family protein

         - label: coding_hmm_lib__hypothetical_equivalog
           type: HMMer3_htab
           path: ${
             var r = "";
             for (var i = 0; i < inputs.hmm_files.length; i++) {
               if (i > 0) {
                 r += ",";
               }
               r += inputs.hmm_files[i].path.replace('file://','');
             }
             return r;
           }
           class: hypoth_equivalog
           index: coding_hmm_lib

         - label: rapsearch2__trusted_full_full
           type: RAPSearch2_m8
           path: ${
             var r = "";
             for (var i = 0; i < inputs.m8_files.length; i++) {
               if (i > 0) {
                 r += ",";
               }
               r += inputs.m8_files[i].path.replace('file://','');
             }
             return r;
           }
           class: trusted
           index: uniref100
           query_cov: 80%
           match_cov: 80%
           percent_identity_cutoff: 50%

         - label: rapsearch2__trusted_partial_full
           type: RAPSearch2_m8
           path: ${
             var r = "";
             for (var i = 0; i < inputs.m8_files.length; i++) {
               if (i > 0) {
                 r += ",";
               }
               r += inputs.m8_files[i].path.replace('file://','');
             }
             return r;
           }
           class: trusted
           index: uniref100
           match_cov: 80%
           percent_identity_cutoff: 50%
           append_text: domain protein

         - label: rapsearch2__trusted_full_partial
           type: RAPSearch2_m8
           path: ${
             var r = "";
             for (var i = 0; i < inputs.m8_files.length; i++) {
               if (i > 0) {
                 r += ",";
               }
               r += inputs.m8_files[i].path.replace('file://','');
             }
             return r;
           }
           class: trusted
           index: uniref100
           query_cov: 80%
           percent_identity_cutoff: 50%
           append_text: domain protein

         - label: rapsearch2__all_full_full
           type: RAPSearch2_m8
           path: ${
             var r = "";
             for (var i = 0; i < inputs.m8_files.length; i++) {
               if (i > 0) {
                 r += ",";
               }
               r += inputs.m8_files[i].path.replace('file://','');
             }
             return r;
           }
           index: uniref100
           query_cov: 80%
           match_cov: 80%
           percent_identity_cutoff: 50%
           prepend_text: putative

         - label: tmhmm
           type: TMHMM
           product_name: putative integral membrane protein
           min_helical_spans: 5
           path: ${
            var r = "";
            for (var i = 0; i < inputs.tmhmm_files.length; i++) {
              if (i > 0) {
              r += ",";
             }
              r += inputs.tmhmm_files[i].path.replace('file://','');
            }
            return r;
          }
    entryname: attributor.config
hints:
- class: DockerRequirement
  dockerPull: jorvis/gales-gce

inputs:
  source_gff3: File
  m8_files: File[]
  hmm_attribute_lookup_file: File
  config_file:
    type: string
    inputBinding:
      prefix: -c
      separate: true
      position: 1
  hmm_files: File[]
  output_format:
    type: string
    inputBinding:
      position: 3
      prefix: -f
      separate: true
  blast_attribute_lookup_file: File
  tmhmm_files: File[]
  output_base:
    type: string
    inputBinding:
      position: 2
      prefix: -o
      separate: true
  polypeptide_fasta: File
outputs:
  the_config:
    type: File
    outputBinding:
      glob: attributor.config
  output_files:
    type:
      type: array
      items: File
    outputBinding:
      glob: $(inputs.output_base + '*')