Mercurial > repos > devteam > ncbi_blast_plus
view tools/ncbi_blast_plus/ncbi_convert2blastmask_wrapper.xml @ 22:6f386c5dc4fb draft
v0.2.01 add -max_hsps, -use_sw_tback; lists args; internal updates
author | peterjc |
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date | Mon, 18 Sep 2017 06:21:27 -0400 |
parents | 3034ce97dd33 |
children | 6f8ea4b9a2c4 |
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<tool id="ncbi_convert2blastmask_wrapper" name="NCBI BLAST+ convert2blastmask" version="@WRAPPER_VERSION@"> <description>Convert masking information in lower-case masked FASTA input to file formats suitable for makeblastdb</description> <macros> <token name="@BINARY@">convert2blastmask</token> <import>ncbi_macros.xml</import> </macros> <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 convert2blastmask -in '$infile' -masking_algorithm '$masking_algorithm' -masking_options '$masking_options' $parse_seqids -out '$outfile' -outfmt $outformat </command> <inputs> <param name="infile" argument="-in" type="data" format="fasta" label="Masked FASTA file"/> <param argument="-masking_algorithm" type="select" label="Used masking algorithm"> <option value="dust">DUST</option> <option value="seg" selected="true">SEG</option> <option value="windowmasker">windowmasker</option> <option value="repeat">repeat</option> <option value="other">other</option> </param> <param argument="-masking_options" type="text" value="" size="20" label="Masking algorithm options to create the masked input" help ="Free text to describe the options used to create the masking files"> <sanitizer invalid_char=""> <valid initial="string.printable" /> </sanitizer> </param> <param argument="-parse_seqids" type="boolean" truevalue="-parse_seqids" falsevalue="" checked="true" label="Parse Seq-ids in FASTA input" help="(-parse_seqids)" /> <param name="outformat" argument="-outfmt" type="select" label="Output format"> <option value="maskinfo_asn1_bin">maskinfo ASN.1 binary</option> <option value="maskinfo_asn1_text" selected="true">maskinfo ASN.1 text</option> <option value="maskinfo_xml">maskinfo_xml</option> </param> </inputs> <outputs> <data name="outfile" format="maskinfo-asn1" label="SEG Masked File"> <change_format> <when input="outformat" value="maskinfo_asn1_bin" format="maskinfo-asn1-binary" /> <!-- <when input="outformat" value="maskinfo_asn1_text" format="maskinfo-asn1" /> --> <when input="outformat" value="maskinfo_xml" format="xml" /> </change_format> </data> </outputs> <tests> <test> <param name="infile" value="four_human_proteins_masked.fasta" ftype="fasta" /> <param name="masking_algorithm" value="seg" /> <param name="masking_options" value="window=12; locut=2.2; hicut=2.5" /> <param name="parse_seqids" value="true" /> <param name="outformat" value="maskinfo_asn1_bin" /> <output name="outfile" file="convert2blastmask_four_human_masked.maskinfo-asn1-binary" /> </test> <test> <param name="infile" value="four_human_proteins_masked.fasta" ftype="fasta" /> <param name="masking_algorithm" value="seg" /> <param name="masking_options" value="window=12; locut=2.2; hicut=2.5" /> <param name="parse_seqids" value="true" /> <param name="outformat" value="maskinfo_asn1_text" /> <output name="outfile" file="convert2blastmask_four_human_masked.maskinfo-asn1" /> </test> </tests> <help> **What it does** Convert masking information in lower-case masked FASTA input to file formats suitable for makeblastdb. More information about segmasker can be found in the `BLAST Command Line Applications User Manual`_. .. _BLAST Command Line Applications User Manual: https://www.ncbi.nlm.nih.gov/books/NBK279690/ **References** If you use this Galaxy tool in work leading to a scientific publication please cite the following papers: @REFERENCES@ </help> <expand macro="blast_citations" /> </tool>