comparison tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml @ 22:6f386c5dc4fb draft

v0.2.01 add -max_hsps, -use_sw_tback; lists args; internal updates

21:7538e2bfcd41

        <token name="@BINARY@">deltablast</token>
        <import>ncbi_macros.xml</import>
    </macros>
    <expand macro="parallelism" />
    <expand macro="preamble" />
    <command>
## The command is a Cheetah template which allows some Python based syntax.
## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
rpsblast
-query "$query"
#if $db_opts.db_opts_selector == "db":
  -db "${db_opts.database.fields.path}"
#elif $db_opts.db_opts_selector == "histdb":
  -db "${os.path.join($db_opts.histdb.files_path,'blastdb')}"
#end if
-evalue $evalue_cutoff
@BLAST_OUTPUT@
@THREADS@
#if $adv_opts.adv_opts_selector=="advanced":

@ADV_QCOV_HSP_PERC@
## End of advanced options:
#end if
    </command>
    <inputs>
        <param name="query" type="data" format="fasta" label="Protein query sequence(s)"/> 

        <expand macro="input_conditional_pssm" />

        <expand macro="input_evalue" />

            <param name="out_format" value="6" />
            <output name="output1" file="empty_file.dat" ftype="tabular" />
        </test>
    </tests>
    <help>
    
@SEARCH_TIME_WARNING@

**What it does**

Search a *protein domain database* using a *protein query*,

*CDD* - NCBI curarated meta-collection of domains, see
http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd_help.shtml#NCBI_curated_domains

*Kog* - PSSMs from automatically aligned sequences and sequence
fragments classified in the KOGs resource, the eukaryotic 
counterpart to COGs, see http://www.ncbi.nlm.nih.gov/COG/

*Cog* - PSSMs from automatically aligned sequences and sequence
fragments classified in the COGs resource, which focuses primarily
on prokaryotes, see http://www.ncbi.nlm.nih.gov/COG/

22:6f386c5dc4fb

        <token name="@BINARY@">deltablast</token>
        <import>ncbi_macros.xml</import>
    </macros>
    <expand macro="parallelism" />
    <expand macro="preamble" />
    <command detect_errors="aggressive">
## The command is a Cheetah template which allows some Python based syntax.
## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
rpsblast
-query '$query'
#if $db_opts.db_opts_selector == "db":
  -db '${db_opts.database.fields.path}'
#elif $db_opts.db_opts_selector == "histdb":
  -db '${os.path.join($db_opts.histdb.files_path, "blastdb")}'
#end if
-evalue $evalue_cutoff
@BLAST_OUTPUT@
@THREADS@
#if $adv_opts.adv_opts_selector=="advanced":

@ADV_QCOV_HSP_PERC@
## End of advanced options:
#end if
    </command>
    <inputs>
        <param argument="-query" type="data" format="fasta" label="Protein query sequence(s)"/>

        <expand macro="input_conditional_pssm" />

        <expand macro="input_evalue" />

            <param name="out_format" value="6" />
            <output name="output1" file="empty_file.dat" ftype="tabular" />
        </test>
    </tests>
    <help>

@SEARCH_TIME_WARNING@

**What it does**

Search a *protein domain database* using a *protein query*,

*CDD* - NCBI curarated meta-collection of domains, see
http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd_help.shtml#NCBI_curated_domains

*Kog* - PSSMs from automatically aligned sequences and sequence
fragments classified in the KOGs resource, the eukaryotic
counterpart to COGs, see http://www.ncbi.nlm.nih.gov/COG/

*Cog* - PSSMs from automatically aligned sequences and sequence
fragments classified in the COGs resource, which focuses primarily
on prokaryotes, see http://www.ncbi.nlm.nih.gov/COG/