Mercurial > repos > devteam > emboss_5
changeset 19:d0847fe9b443 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 18de4aa9ba00124b1b3e3afe14219e46931e58a9"
| author | iuc |
|---|---|
| date | Fri, 09 Jul 2021 18:35:00 +0000 |
| parents | c2228166c035 |
| children | 21a9fb508031 |
| files | emboss_fuzznuc.xml test-data/emboss_fuzznuc_out2.tabular |
| diffstat | 2 files changed, 63 insertions(+), 2 deletions(-) [+] |
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--- a/emboss_fuzznuc.xml Fri Nov 20 16:49:40 2020 +0000 +++ b/emboss_fuzznuc.xml Fri Jul 09 18:35:00 2021 +0000 @@ -1,11 +1,35 @@ -<tool id="EMBOSS: fuzznuc37" name="fuzznuc" version="5.0.2"> +<tool id="EMBOSS: fuzznuc37" name="fuzznuc" version="5.0.3"> <description>Nucleic acid pattern search</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements" /> <code file="emboss_format_corrector.py" /> - <command>fuzznuc -sequence '$input1' -outfile '$out_file1' -pattern '$pattern' -pmismatch $mismatch -complement $complement -rformat2 $out_format1 -auto</command> + <command><![CDATA[ + fuzznuc + + -sequence '$input1' + $seq_qualifiers.sreverse1 $seq_qualifiers.snucleotide1 $seq_qualifiers.sprotein1 $seq_qualifiers.slower1 $seq_qualifiers.supper1 + #if $seq_qualifiers.sbegin1 + -sbegin1 '$seq_qualifiers.sbegin1' + #end if + #if $seq_qualifiers.send1 + -send1 '$seq_qualifiers.send1' + #end if + + -outfile '$out_file1' + $out_qualifiers.raccshow2 $out_qualifiers.rdesshow2 $out_qualifiers.rscoreshow2 $out_qualifiers.rusashow2 + #if $out_qualifiers.rmaxall2 + -rmaxall2 '$out_qualifiers.rmaxall2' + #end if + #if $out_qualifiers.rmaxseq2 + -rmaxseq2 '$out_qualifiers.rmaxseq2' + #end if + + -pattern '$pattern' -pmismatch '$mismatch' -rformat2 '$out_format1' -auto + + -complement '$complement' + ]]></command> <inputs> <param name="input1" type="data" format="fasta" label="Sequences" /> <param name="pattern" type="text" value="" label="Search pattern"> @@ -42,6 +66,26 @@ <option value="table">Table</option> <option value="tagseq">TagSeq</option> </param> + + <section name="seq_qualifiers" title="Sequence associated qualifiers"> + <param type="integer" argument="-sbegin1" optional="true" label="Start of each sequence to be used"/> + <param type="integer" argument="-send1" optional="true" label="End of each sequence to be used"/> + <param type="boolean" argument="-sreverse1" truevalue="-sreverse1 Y" falsevalue="" label="Reverse (if DNA)"/> + <param type="boolean" argument="-snucleotide1" truevalue="-snucleotide1 Y" falsevalue="" label="Sequence is nucleotide"/> + <param type="boolean" argument="-sprotein1" truevalue="-sprotein1 Y" falsevalue="" label="Sequence is protein"/> + <param type="boolean" argument="-slower1" truevalue="-slower1 Y" falsevalue="" label="Make lower case"/> + <param type="boolean" argument="-supper1" truevalue="-supper1 Y" falsevalue="" label="Make upper case"/> + </section> + + <section name="out_qualifiers" title="Outfile associated qualifiers"> + <param type="boolean" argument="-raccshow2" truevalue="-raccshow2 Y" falsevalue="" label="Show accession number in the report"/> + <param type="boolean" argument="-rdesshow2" truevalue="-rdesshow2 Y" falsevalue="" label="Show description in the report"/> + <param type="boolean" argument="-rscoreshow2" truevalue="-rscoreshow2 Y" falsevalue="" label="Show the score in the report"/> + <param type="boolean" argument="-rusashow2" truevalue="-rusashow2 Y" falsevalue="" label="Show the full USA in the report"/> + <param type="integer" argument="-rmaxall2" optional="true" label="Maximum total hits to report"/> + <param type="integer" argument="-rmaxseq2" optional="true" label="Maximum hits to report for one sequence"/> + </section> + </inputs> <outputs> <data name="out_file1" format="fuzznuc" /> @@ -55,6 +99,17 @@ <param name="out_format1" value="excel"/> <output name="out_file1" file="emboss_fuzznuc_out.tabular"/> </test> + <test> + <param name="input1" value="2.fasta"/> + <param name="pattern" value="AA"/> + <param name="mismatch" value="0"/> + <param name="complement" value="no"/> + <param name="out_format1" value="excel"/> + <param name="seq_qualifiers|supper1" value="true"/> + <param name="seq_qualifiers|sbegin1" value="100"/> + <param name="out_qualifiers|rmaxseq2" value="5"/> + <output name="out_file1" file="emboss_fuzznuc_out2.tabular"/> + </test> </tests> <help> .. class:: warningmark
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/emboss_fuzznuc_out2.tabular Fri Jul 09 18:35:00 2021 +0000 @@ -0,0 +1,6 @@ +SeqName Start End Score Strand Pattern_name Mismatch +Sequence 157 158 2 + pattern1 . +Sequence 158 159 2 + pattern1 . +Sequence 181 182 2 + pattern1 . +Sequence 193 194 2 + pattern1 . +Sequence 196 197 2 + pattern1 .