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comparison maker.xml @ 7:10e2edf1e1fb draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 38b61f14db4a6e474c55e6107e31eaba6c677ad9"
author iuc
date Tue, 22 Jun 2021 10:14:40 +0000
parents b7ad44afd7b0
children d3b3de98c481
comparison
equal deleted inserted replaced
6:b7ad44afd7b0 7:10e2edf1e1fb
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="maker" name="Maker" profile="16.04" version="@VERSION@"> 2 <tool id="maker" name="Maker" profile="16.04" version="@VERSION@+galaxy@SUFFIX_VERSION@">
3 <description>genome annotation pipeline</description> 3 <description>genome annotation pipeline</description>
4 <macros> 4 <macros>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements"/> 7 <expand macro="requirements"/>
42 MPI_CMD="" && 42 MPI_CMD="" &&
43 if [ "\$MAKER_MPI" == "1" ]; then 43 if [ "\$MAKER_MPI" == "1" ]; then
44 MPI_CMD="mpiexec -n \${GALAXY_SLOTS:-4}"; 44 MPI_CMD="mpiexec -n \${GALAXY_SLOTS:-4}";
45 fi && 45 fi &&
46 46
47 \${MPI_CMD} maker --ignore_nfs_tmp maker_opts.ctl maker_bopts.ctl maker_exe.ctl < /dev/null 47 \${MPI_CMD} maker --ignore_nfs_tmp $advanced.fix_nucleotides maker_opts.ctl maker_bopts.ctl maker_exe.ctl < /dev/null
48 48
49 && 49 &&
50 50
51 gff3_merge -d *.maker.output/*_master_datastore_index.log -o '${output_full}' 51 gff3_merge -d *.maker.output/*_master_datastore_index.log -o '${output_full}'
52 52
451 <param name="trna" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Find tRNAs with tRNAscan"/> 451 <param name="trna" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Find tRNAs with tRNAscan"/>
452 <param name="snoscan_rrna" type="data" format="fasta" label="rRNA file to have Snoscan find snoRNAs" optional="True"/> 452 <param name="snoscan_rrna" type="data" format="fasta" label="rRNA file to have Snoscan find snoRNAs" optional="True"/>
453 </section> 453 </section>
454 454
455 <section name="advanced" title="Advanced settings" expanded="False"> 455 <section name="advanced" title="Advanced settings" expanded="False">
456 <param name="fix_nucleotides" argument="-fix_nucleotides" type="boolean" truevalue="-fix_nucleotides" falsevalue="" checked="false" label="Fix nucleotides" help="This will replace non-IUPAC characters with 'N's."/>
456 <param name="other_gff" type="data" format="gff" label="Extra features to pass-through to final Maker generated GFF3 file" optional="True"/> 457 <param name="other_gff" type="data" format="gff" label="Extra features to pass-through to final Maker generated GFF3 file" optional="True"/>
457 <param name="alt_peptide" type="text" value="C" size="1" label="Amino acid used to replace non-standard amino acids in BLAST databases"> 458 <param name="alt_peptide" type="text" value="C" size="1" label="Amino acid used to replace non-standard amino acids in BLAST databases">
458 <validator type="regex" message="This must be a single uppercase letter">^[A-Z]$</validator> 459 <validator type="regex" message="This must be a single uppercase letter">^[A-Z]$</validator>
459 </param> 460 </param>
460 <param name="max_dna_len" type="integer" value="100000" label="Length for dividing up contigs into chunks" help="Increases/decreases memory usage"/> 461 <param name="max_dna_len" type="integer" value="100000" label="Length for dividing up contigs into chunks" help="Increases/decreases memory usage"/>
561 <param name="repeat_masking|repeat_source|dfam_lib" value="Dfam_partial_test.h5" ftype="h5" /> 562 <param name="repeat_masking|repeat_source|dfam_lib" value="Dfam_partial_test.h5" ftype="h5" />
562 <param name="repeat_masking|repeat_source|species_name" value="rodent" /> 563 <param name="repeat_masking|repeat_source|species_name" value="rodent" />
563 <output name="output_gff" file="annot_dfam_up.gff3"/> 564 <output name="output_gff" file="annot_dfam_up.gff3"/>
564 <output name="output_evidences" file="evidences_norm_dfam_up.gff3" compare="sim_size"/> 565 <output name="output_evidences" file="evidences_norm_dfam_up.gff3" compare="sim_size"/>
565 </test> 566 </test>
567 <test>
568 <param name="genome" value="genome.fasta"/>
569 <param name="est_evidences|est" value="non_IUPAC.fasta"/>
570 <param name="est_evidences|est2genome" value="1"/>
571 <param name="repeat_masking|repeat_source|source_type" value="no"/>
572 <param name="advanced|fix_nucleotides" value="true"/>
573 <output name="output_gff" file="annot_fix_nucleotides.gff3"/>
574 <output name="output_evidences" file="evidences_fix_nucletides.gff3" compare="sim_size"/>
575 </test>
566 </tests> 576 </tests>
567 <help><![CDATA[ 577 <help><![CDATA[
568 MAKER is a portable and easily configurable genome annotation pipeline. Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. MAKER identifies repeats, aligns ESTs and proteins to a genome, produces ab-initio gene predictions and automatically synthesizes these data into gene annotations having evidence-based quality values. MAKER is also easily trainable: outputs of preliminary runs can be used to automatically retrain its gene prediction algorithm, producing higher quality gene-models on seusequent runs. MAKER's inputs are minimal and its ouputs can be directly loaded into a GMOD database. They can also be viewed in the Apollo genome browser; this feature of MAKER provides an easy means to annotate, view and edit individual contigs and BACs without the overhead of a database. MAKER should prove especially useful for emerging model organism projects with minimal bioinformatics expertise and computer resources. 578 MAKER is a portable and easily configurable genome annotation pipeline. Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. MAKER identifies repeats, aligns ESTs and proteins to a genome, produces ab-initio gene predictions and automatically synthesizes these data into gene annotations having evidence-based quality values. MAKER is also easily trainable: outputs of preliminary runs can be used to automatically retrain its gene prediction algorithm, producing higher quality gene-models on seusequent runs. MAKER's inputs are minimal and its ouputs can be directly loaded into a GMOD database. They can also be viewed in the Apollo genome browser; this feature of MAKER provides an easy means to annotate, view and edit individual contigs and BACs without the overhead of a database. MAKER should prove especially useful for emerging model organism projects with minimal bioinformatics expertise and computer resources.
569 579
570 .. _Maker: http://www.yandell-lab.org/software/maker.html 580 .. _Maker: http://www.yandell-lab.org/software/maker.html