diff tiptoft.xml @ 0:7987b0437fe1 draft default tip

"planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/tiptoft commit fae924375dd50aec403ad6bf632f2a8ffeac3863-dirty"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tiptoft.xml	Fri Jan 10 14:17:18 2020 +0000
@@ -0,0 +1,95 @@
+<tool id="tiptoft" name="tiptoft" version="@VERSION@">
+    <description>Plasmid replicon and incompatibility group prediction from uncorrected long reads</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="version_command" />
+    <command detect_errors="exit_code"><![CDATA[
+        tiptoft
+        #if str($opt_input.plasmid_data) != ""
+            --plasmid_data '$plasmid_data'
+        #end if
+        --kmer $opt_input.kmer
+        #if str($opt_output.filtered_reads_file) != ""
+        --filtered_reads_file $opt_output.filtered_reads_file
+        #end if
+        #if str($opt_output.output_file) != ""
+        --output_file $opt_output.output_file
+        #end if
+         #if $opt_adv.no_hc_compression
+        --no_hc_compression
+        #end if
+        #if $opt_adv.no_gene_filter
+        --no_gene_filter
+        #end if
+        --max_gap $opt_adv.max_gap
+        --max_kmer_count $opt_adv.max_kmer_count
+        --margin $opt_adv.margin
+        --min_block_size $opt_adv.min_block_size
+        --min_fasta_hits $opt_adv.min_fasta_hits
+        --min_perc_coverage $opt_adv.min_perc_coverage
+        --min_kmers_for_onex_pass $opt_adv.min_kmers_for_onex_pass
+        '$fastq' > '$output'
+    ]]></command>
+    
+    <inputs>
+       <param name="fastq" type="data" format="fastqsanger,fastqsanger.gz" label="Select fastq dataset" help="Specify dataset with single reads"/>
+        
+        <section name="opt_input" title="Optional Input">
+        <param name="plasmid_data" argument="--plasmid_data" type="data" format="fasta" label="Plasmid database" help="A fasta file containing plasmid data. Defaults to bundled database"/>
+        <param argument="--kmer" type="integer" value="13" label="K-mer size" help="Default: 13"/>
+        </section>
+
+        <section name="opt_output" title="Optional Output">
+        <param argument="--filtered_reads_file" type="text" value="" label="Filename to save matching reads to" help="Default: None" />
+        <param argument="--output_file" type="text" value="" label="Output file" help="Default: None" />
+        </section>
+
+        <section name="opt_adv" title="Optional Advanced Input Arguments">
+        <param argument="--no_hc_compression" type="boolean" truevalue="--no_hc_compression" falsevalue="" checked="false" label="Turn off homoploymer compression of k-mers" help="Default:No" />
+        <param argument="--no_gene_filter" type="boolean" truevalue="--no_gene_filter" falsevalue="" checked="false" label="Dont filter out lower coverage genes from same group" help="Default:No" />
+        <param argument="--max_gap" type="integer" value="3" label="Maximum gap for blocks to be contigous, measured in
+                        multiples of the k-mer size" help="Default:3" />
+        <param argument="--max_kmer_count" type="integer" value="10" label="Exclude k-mers which occur more than this number of
+                        times in a sequence" help="Default:10" />
+        <param argument="--margin" type="integer" value="10" label="Flanking region around a block to use for mapping" help="Default:10" />
+        <param argument="--min_block_size" type="integer" value="50" label="Minimum block size in bases" help="Default:10" />
+        <param argument="--min_fasta_hits" type="integer" value="8" label="Minimum No. of kmers matching a read" help="Default:8" />
+        <param argument="--min_perc_coverage" type="integer" value="8" label="Minimum percentage coverage of typing sequence to
+                        report" help="Default:85" />
+        <param argument="--min_kmers_for_onex_pass" type="integer" value="5" label="Minimum No. of kmers matching a read in 1st pass" help="Default:5" />
+        </section>
+    </inputs>
+
+    <outputs>
+        <data name="output" format="tabular" label="${tool.name} on ${on_string} report file" />
+    </outputs>
+
+    <tests>
+        <test>
+             <param name="fastq" value="query_gz.fastq" ftype="fastqsanger"/>
+             <param name="plasmid_data" value="plasmid.fa" ftype="fasta"/>
+             <output name="output" file="expected_outputfile" ftype="tabular" />
+        </test>
+    </tests>
+    <help><![CDATA[
+    usage: tiptoft [options] input.fastq
+
+    Plasmid replicon and incompatibility group prediction from uncorrected long
+    reads
+
+    Documentation can be found at `<https://github.com/andrewjpage/tiptoft>`_.
+
+    ]]></help>
+    <citations>
+        <citation type="bibtex">
+@UNPUBLISHED{Page2018,
+    author = {Page, Andrew},
+    title = {tiptoft: Predict plasmids from uncorrected long read data},
+    year = {2018},
+    url = {https://github.com/andrewjpage/tiptoft},
+}
+        </citation>
+    </citations>
+</tool>