Mercurial > repos > bgruening > bionano_scaffold
comparison bionano_scaffold.xml @ 7:42b12498bfa6 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bionano commit 25785fac3064e7def7ebccd45d452dc0b22ec89a"
| author | bgruening |
|---|---|
| date | Sat, 05 Feb 2022 18:14:21 +0000 |
| parents | b0c441b90e23 |
| children | 7ce0622eb07c |
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| 6:b0c441b90e23 | 7:42b12498bfa6 |
|---|---|
| 4 <import>macros.xml</import> | 4 <import>macros.xml</import> |
| 5 </macros> | 5 </macros> |
| 6 <expand macro="edam_ontology"/> | 6 <expand macro="edam_ontology"/> |
| 7 <expand macro="requirements"/> | 7 <expand macro="requirements"/> |
| 8 <command detect_errors="exit_code"><![CDATA[ | 8 <command detect_errors="exit_code"><![CDATA[ |
| 9 #set RefAligner = '/usr/local/bin/RefAligner' | 9 #set RefAligner = '/RefAligner/RefAligner' |
| 10 #set output_file_NCBI = 'hybrid_scaffolds/bionano_bppAdjust_cmap_ngs_fasta_NGScontigs_HYBRID_SCAFFOLD_NCBI.fasta' | 10 #set output_file_NCBI = 'hybrid_scaffolds/bionano_bppAdjust_cmap_ngs_fasta_NGScontigs_HYBRID_SCAFFOLD_NCBI.fasta' |
| 11 #set output_file_not_scaffolded = 'hybrid_scaffolds/bionano_bppAdjust_cmap_ngs_fasta_NGScontigs_HYBRID_SCAFFOLD_NOT_SCAFFOLDED.fasta' | 11 #set output_file_not_scaffolded = 'hybrid_scaffolds/bionano_bppAdjust_cmap_ngs_fasta_NGScontigs_HYBRID_SCAFFOLD_NOT_SCAFFOLDED.fasta' |
| 12 ## softlinks do not work | 12 ## softlinks do not work |
| 13 cp '${ngs_fasta}' ./ngs.fasta | 13 cp '${ngs_fasta}' ./ngs.fasta |
| 14 && cp '${bionano_cmap}' ./bionano.cmap | 14 && cp '${bionano_cmap}' ./bionano.cmap |
| 54 ###end if | 54 ###end if |
| 55 -f | 55 -f |
| 56 $zip_file | 56 $zip_file |
| 57 -o ./ | 57 -o ./ |
| 58 #if $trim_cut_sites | 58 #if $trim_cut_sites |
| 59 && export PATH=/opt/conda/bin/:\$PATH | |
| 59 && python '$__tool_directory__/remove_fake_cut_sites.py' $output_file_NCBI 'SCAFFOLD_NCBI_trimmed.fasta' 'output.log' | 60 && python '$__tool_directory__/remove_fake_cut_sites.py' $output_file_NCBI 'SCAFFOLD_NCBI_trimmed.fasta' 'output.log' |
| 60 && python '$__tool_directory__/remove_fake_cut_sites.py' $output_file_not_scaffolded 'NOT_SCAFFOLDED_trimmed.fasta' 'output.log' | 61 && python '$__tool_directory__/remove_fake_cut_sites.py' $output_file_not_scaffolded 'NOT_SCAFFOLDED_trimmed.fasta' 'output.log' |
| 61 #end if | 62 #end if |
| 62 ]]> </command> | 63 ]]> </command> |
| 63 <configfiles> | 64 <configfiles> |
| 470 <has_text text="alignmentOrientation" /> | 471 <has_text text="alignmentOrientation" /> |
| 471 </assert_contents> | 472 </assert_contents> |
| 472 </output> | 473 </output> |
| 473 <output name="results" ftype="zip"> | 474 <output name="results" ftype="zip"> |
| 474 <assert_contents> | 475 <assert_contents> |
| 475 <!--<has_size value="4231746" delta="300" />--> | |
| 476 <has_archive_member path=".*/status.txt"/> | 476 <has_archive_member path=".*/status.txt"/> |
| 477 </assert_contents> | 477 </assert_contents> |
| 478 </output> | 478 </output> |
| 479 <assert_stdout> | 479 <assert_stdout> |
| 480 <has_text_matching expression='attr="maxmem" val0="\d+"'/> | 480 <has_text_matching expression='attr="maxmem" val0="\d+"'/> |
| 538 <assert_stdout> | 538 <assert_stdout> |
| 539 <has_text_matching expression='attr="maxvirtmem" val0="\d+"'/> | 539 <has_text_matching expression='attr="maxvirtmem" val0="\d+"'/> |
| 540 </assert_stdout> | 540 </assert_stdout> |
| 541 <assert_stdout> | 541 <assert_stdout> |
| 542 <has_text text="hybridScaffold"/> | 542 <has_text text="hybridScaffold"/> |
| 543 <!--attribute_is path="hybridScaffold/global/flag[@attr='maxthreads']" attribute="val0" text="2"/--> | |
| 544 </assert_stdout> | 543 </assert_stdout> |
| 545 </test> | 544 </test> |
| 546 <test expect_num_outputs="6"> | 545 <test expect_num_outputs="6"> |
| 547 <param name="ngs_fasta" value="assembly.fasta.gz"/> | 546 <param name="ngs_fasta" value="assembly.fasta.gz"/> |
| 548 <param name="bionano_cmap" value="colormap_assembly.cmap"/> | 547 <param name="bionano_cmap" value="colormap_assembly.cmap"/> |
| 579 <has_text text="alignmentOrientation" /> | 578 <has_text text="alignmentOrientation" /> |
| 580 </assert_contents> | 579 </assert_contents> |
| 581 </output> | 580 </output> |
| 582 <output name="results" ftype="zip"> | 581 <output name="results" ftype="zip"> |
| 583 <assert_contents> | 582 <assert_contents> |
| 584 <!--<has_size value="4231908" delta="300" />--> | |
| 585 <has_archive_member path=".*/status.txt"/> | 583 <has_archive_member path=".*/status.txt"/> |
| 586 </assert_contents> | 584 </assert_contents> |
| 587 </output> | 585 </output> |
| 588 <assert_stdout> | 586 <assert_stdout> |
| 589 <has_text_matching expression='attr="maxmem" val0="\d+"'/> | 587 <has_text_matching expression='attr="maxmem" val0="\d+"'/> |