Mercurial > repos > thanhlv > bin3c
comparison cluster.xml @ 16:cdfc397e7b0f draft
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit 979c715c9d69fe906eead3270f26cd029c7eb8af-dirty
| author | thanhlv |
|---|---|
| date | Thu, 17 Oct 2019 12:41:47 -0400 |
| parents | e0c0decc7ec0 |
| children | 0e9275cd89a6 |
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| 15:e0c0decc7ec0 | 16:cdfc397e7b0f |
|---|---|
| 12 --min-reflen $min_reflen | 12 --min-reflen $min_reflen |
| 13 --min-signal $min_signal | 13 --min-signal $min_signal |
| 14 -s 201987356473 | 14 -s 201987356473 |
| 15 --assembler $assembler | 15 --assembler $assembler |
| 16 $no_report | 16 $no_report |
| 17 $no_spades | |
| 18 $no_plot | 17 $no_plot |
| 19 $no_fasta | 18 $no_fasta |
| 20 $only_large | 19 $only_large |
| 21 $fasta | 20 $fasta |
| 21 --n-iter $iteration | |
| 22 $contact_map out | 22 $contact_map out |
| 23 ]]> </command> | 23 ]]> </command> |
| 24 | 24 |
| 25 <inputs> | 25 <inputs> |
| 26 <param name="contact_map" type="data" format="tar.gz" label="Contact map" help="This file is generated from mkmap command" /> | 26 <param name="contact_map" type="data" format="tar.gz" label="Contact map" help="This file is generated from mkmap command" /> |
| 31 </param> | 31 </param> |
| 32 <param name="max_image" type="integer" min="1" value="4000" label="Maximum image size for plots"/> | 32 <param name="max_image" type="integer" min="1" value="4000" label="Maximum image size for plots"/> |
| 33 <param name="min_extent" type="integer" min="1" value="50000" label="Minimum cluster extent used in output"/> | 33 <param name="min_extent" type="integer" min="1" value="50000" label="Minimum cluster extent used in output"/> |
| 34 <param name="min_reflen" type="integer" min="1" value="1000" label="Minimum acceptable reference length"/> | 34 <param name="min_reflen" type="integer" min="1" value="1000" label="Minimum acceptable reference length"/> |
| 35 <param name="min_signal" type="integer" min="1" value="5" label="Minimum acceptable signal"/> | 35 <param name="min_signal" type="integer" min="1" value="5" label="Minimum acceptable signal"/> |
| 36 <param name="iteration" type="integer" min="1" value="10" label="Number of iterations for clustering optimisation"/> | |
| 36 <param name="no_report" type="boolean" truevalue="--no-report" falsevalue="" checked="false" label="Do not generate a cluster report" /> | 37 <param name="no_report" type="boolean" truevalue="--no-report" falsevalue="" checked="false" label="Do not generate a cluster report" /> |
| 37 <param name="no_spades" type="boolean" truevalue="--no-spades" falsevalue="" checked="false" label="Assembly was not done using SPAdes" /> | |
| 38 <param name="no_plot" type="boolean" truevalue="--no-plot" falsevalue="" checked="false" label="Do not generate a clustered heatmap" /> | 38 <param name="no_plot" type="boolean" truevalue="--no-plot" falsevalue="" checked="false" label="Do not generate a clustered heatmap" /> |
| 39 <param name="no_fasta" type="boolean" truevalue="--no-fasta" falsevalue="" checked="false" label="Do not generate cluster FASTA files" /> | 39 <param name="no_fasta" type="boolean" truevalue="--no-fasta" falsevalue="" checked="false" label="Do not generate cluster FASTA files" /> |
| 40 <param name="only_large" type="boolean" truevalue="--only-large" falsevalue="" checked="false" label="Only write FASTA for clusters longer than min_extent" /> | 40 <param name="only_large" type="boolean" truevalue="--only-large" falsevalue="" checked="false" label="Only write FASTA for clusters longer than min_extent" /> |
| 41 <param name="fasta" type="data" format="fasta" label="Alternative source FASTA location from that supplied during mkmap" /> | 41 <param name="fasta" type="data" format="fasta,fastq.gz" label="Alternative source FASTA from that supplied during mkmap" /> |
| 42 </inputs> | 42 </inputs> |
| 43 | 43 |
| 44 <outputs> | 44 <outputs> |
| 45 <data name="log" format="text" label="{tool.name} on ${on_string} Log" from_work_dir="out/bin3C.log"/> | 45 <data name="log" format="text" label="{tool.name} on ${on_string} Log" from_work_dir="out/bin3C.log"/> |
| 46 <data name="clustering_mcl" format="binary" label="{tool.name} on ${on_string} Clustering solution in MCL format" from_work_dir="out/clustering.mcl"/> | 46 <data name="clustering_mcl" format="binary" label="{tool.name} on ${on_string} Clustering solution in MCL format" from_work_dir="out/clustering.mcl"/> |