Mercurial > repos > devteam > ncbi_blast_plus
comparison 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 |
|---|---|
| date | Mon, 18 Sep 2017 06:21:27 -0400 |
| parents | 3034ce97dd33 |
| children | 6f8ea4b9a2c4 |
comparison
equal
deleted
inserted
replaced
| 21:7538e2bfcd41 | 22:6f386c5dc4fb |
|---|---|
| 3 <macros> | 3 <macros> |
| 4 <token name="@BINARY@">convert2blastmask</token> | 4 <token name="@BINARY@">convert2blastmask</token> |
| 5 <import>ncbi_macros.xml</import> | 5 <import>ncbi_macros.xml</import> |
| 6 </macros> | 6 </macros> |
| 7 <expand macro="preamble" /> | 7 <expand macro="preamble" /> |
| 8 <command> | 8 <command detect_errors="aggressive"> |
| 9 ## The command is a Cheetah template which allows some Python based syntax. | 9 ## The command is a Cheetah template which allows some Python based syntax. |
| 10 ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces | 10 ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces |
| 11 convert2blastmask | 11 convert2blastmask |
| 12 -in $infile | 12 -in '$infile' |
| 13 -masking_algorithm "$masking_algorithm" | 13 -masking_algorithm '$masking_algorithm' |
| 14 -masking_options "$masking_options" | 14 -masking_options '$masking_options' |
| 15 $parse_seqids | 15 $parse_seqids |
| 16 -out "$outfile" | 16 -out '$outfile' |
| 17 -outfmt $outformat | 17 -outfmt $outformat |
| 18 </command> | 18 </command> |
| 19 <inputs> | 19 <inputs> |
| 20 <param name="infile" type="data" format="fasta" label="masked FASTA file"/> | 20 <param name="infile" argument="-in" type="data" format="fasta" label="Masked FASTA file"/> |
| 21 <param name="masking_algorithm" type="select" label="Used masking algorithm"> | 21 <param argument="-masking_algorithm" type="select" label="Used masking algorithm"> |
| 22 <option value="dust">DUST</option> | 22 <option value="dust">DUST</option> |
| 23 <option value="seg" selected="true">SEG</option> | 23 <option value="seg" selected="true">SEG</option> |
| 24 <option value="windowmasker">windowmasker</option> | 24 <option value="windowmasker">windowmasker</option> |
| 25 <option value="repeat">repeat</option> | 25 <option value="repeat">repeat</option> |
| 26 <option value="other">other</option> | 26 <option value="other">other</option> |
| 27 </param> | 27 </param> |
| 28 <param name="masking_options" type="text" value="" size="20" label="Masking algorithm options to create the masked input" | 28 <param argument="-masking_options" type="text" value="" size="20" label="Masking algorithm options to create the masked input" |
| 29 help ="free text to describe the options used to create the masking files. (-masking_options)"> | 29 help ="Free text to describe the options used to create the masking files"> |
| 30 <sanitizer invalid_char=""> | 30 <sanitizer invalid_char=""> |
| 31 <valid initial="string.printable" /> | 31 <valid initial="string.printable" /> |
| 32 </sanitizer> | 32 </sanitizer> |
| 33 </param> | 33 </param> |
| 34 <param name="parse_seqids" type="boolean" truevalue="-parse_seqids" falsevalue="" checked="true" label="Parse Seq-ids in FASTA input" help="(-parse_seqids)" /> | 34 <param argument="-parse_seqids" type="boolean" truevalue="-parse_seqids" falsevalue="" checked="true" label="Parse Seq-ids in FASTA input" help="(-parse_seqids)" /> |
| 35 <param name="outformat" type="select" label="Output format"> | 35 <param name="outformat" argument="-outfmt" type="select" label="Output format"> |
| 36 <option value="maskinfo_asn1_bin">maskinfo ASN.1 binary</option> | 36 <option value="maskinfo_asn1_bin">maskinfo ASN.1 binary</option> |
| 37 <option value="maskinfo_asn1_text" selected="True">maskinfo ASN.1 text</option> | 37 <option value="maskinfo_asn1_text" selected="true">maskinfo ASN.1 text</option> |
| 38 <option value="maskinfo_xml">maskinfo_xml</option> | 38 <option value="maskinfo_xml">maskinfo_xml</option> |
| 39 </param> | 39 </param> |
| 40 </inputs> | 40 </inputs> |
| 41 <outputs> | 41 <outputs> |
| 42 <data name="outfile" format="maskinfo-asn1" label="SEG Masked File"> | 42 <data name="outfile" format="maskinfo-asn1" label="SEG Masked File"> |
| 43 <change_format> | 43 <change_format> |
| 44 <when input="outformat" value="maskinfo_asn1_bin" format="maskinfo-asn1-binary" /> | 44 <when input="outformat" value="maskinfo_asn1_bin" format="maskinfo-asn1-binary" /> |
| 45 <!-- | 45 <!-- |
| 46 <when input="outformat" value="maskinfo_asn1_text" format="maskinfo-asn1" /> | 46 <when input="outformat" value="maskinfo_asn1_text" format="maskinfo-asn1" /> |
| 47 --> | 47 --> |
| 48 <when input="outformat" value="maskinfo_xml" format="xml" /> | 48 <when input="outformat" value="maskinfo_xml" format="xml" /> |
| 49 </change_format> | 49 </change_format> |
| 50 </data> | 50 </data> |
| 51 </outputs> | 51 </outputs> |
| 52 <tests> | 52 <tests> |
| 53 <test> | 53 <test> |
| 54 <param name="infile" value="four_human_proteins_masked.fasta" ftype="fasta" /> | 54 <param name="infile" value="four_human_proteins_masked.fasta" ftype="fasta" /> |
| 55 <param name="masking_algorithm" value="seg" /> | 55 <param name="masking_algorithm" value="seg" /> |
| 56 <param name="masking_options" value="window=12; locut=2.2; hicut=2.5" /> | 56 <param name="masking_options" value="window=12; locut=2.2; hicut=2.5" /> |
| 57 <param name="parse_seqids" value="True" /> | 57 <param name="parse_seqids" value="true" /> |
| 58 <param name="outformat" value="maskinfo_asn1_bin" /> | 58 <param name="outformat" value="maskinfo_asn1_bin" /> |
| 59 <output name="outfile" file="convert2blastmask_four_human_masked.maskinfo-asn1-binary" /> | 59 <output name="outfile" file="convert2blastmask_four_human_masked.maskinfo-asn1-binary" /> |
| 60 </test> | 60 </test> |
| 61 <test> | 61 <test> |
| 62 <param name="infile" value="four_human_proteins_masked.fasta" ftype="fasta" /> | 62 <param name="infile" value="four_human_proteins_masked.fasta" ftype="fasta" /> |
| 63 <param name="masking_algorithm" value="seg" /> | 63 <param name="masking_algorithm" value="seg" /> |
| 64 <param name="masking_options" value="window=12; locut=2.2; hicut=2.5" /> | 64 <param name="masking_options" value="window=12; locut=2.2; hicut=2.5" /> |
| 65 <param name="parse_seqids" value="True" /> | 65 <param name="parse_seqids" value="true" /> |
| 66 <param name="outformat" value="maskinfo_asn1_text" /> | 66 <param name="outformat" value="maskinfo_asn1_text" /> |
| 67 <output name="outfile" file="convert2blastmask_four_human_masked.maskinfo-asn1" /> | 67 <output name="outfile" file="convert2blastmask_four_human_masked.maskinfo-asn1" /> |
| 68 </test> | 68 </test> |
| 69 </tests> | 69 </tests> |
| 70 <help> | 70 <help> |