diff macros.xml @ 0:47cea67b74ea draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/khmer/ commit be9a20423d1a6ec33d59341e0e61b535127bbce2

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Wed Nov 11 09:47:17 2015 -0500
@@ -0,0 +1,148 @@
+<macros>
+    <token name="@WRAPPER_VERSION@">2.0</token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@WRAPPER_VERSION@">khmer</requirement>
+        </requirements>
+    </xml>
+    <xml name="version">
+        <version_command><![CDATA[@BINARY@ --version 2>&1 | tail -n 1 | cut -d ' ' -f 2]]></version_command>
+    </xml>
+    <xml name="stdio">
+        <stdio>
+            <exit_code range="1:" level="fatal" />
+        </stdio>
+    </xml>
+    <token name="@TABLEPARAMS@">
+<![CDATA[
+#if $parameters.type == "simple"
+  --ksize=20
+  --n_tables=4
+  --max-tablesize=$parameters.tablesize
+#else
+  --ksize=$parameters.ksize
+  --n_tables=$parameters.n_tables
+  --max-tablesize="$parameters.tablesize_specific"
+#end if
+]]>
+    </token>
+    <token name="@THREADS@">--threads \${GALAXY_SLOTS:-4}</token>
+    <xml name="tableinputs">
+        <conditional name="parameters">
+            <param name="type" type="select" label="Advanced Parameters"
+                help="ksize, n_tables, a specific tablesize" >
+                <option value="simple" selected="true">Hide</option>
+                <option value="specific">Show</option>
+            </param>
+            <when value="simple">
+                <param name="tablesize" type="select" label="Sample Type" display="radio">
+                    <option value="1e9" selected="true">Microbial Genome</option>
+                    <option value="2e9">Animal Transcriptome</option>
+                    <option value="4e9">Small Animal Genome or Low-Diversity Metagenome</option>
+                    <option value="16e9">Large Animal Genome</option>
+                </param>
+            </when>
+            <when value="specific">
+                <param name="ksize" type="integer" value="20" label="k-mer size" help="k-mer size to use" />
+                <param name="n_tables" type="integer" min="1" value="4" label="n_tables" help="number of tables to use" />
+                <param name="tablesize_specific" type="text" value="1000000.0" 
+                    label="tablesize" help="(--max-tablesize) upper bound on the tablesize to use" />
+            </when>
+        </conditional>
+    </xml>
+    <xml name="input_sequences_filenames">
+        <param  name="inputs" multiple="true" type="data" format="fasta,fastq"
+            label="Sequences in FASTA or FASTQ format"
+            help="Put in order of precedence such as longest reads first." />
+    </xml>
+    <xml name="input_sequence_filename">
+        <param  name="input_sequence_filename" type="data" format="fasta,fastq"
+            label="Sequence in FASTA or FASTQ format" />
+    </xml>
+    <xml name="input_countgraph_filename">
+        <param  name="input_countgraph_filename" type="data" format="oxlicg"
+            label="the k-mer countgraph to query"
+            help="The abundances of the k-mers in the input nucleotide sequence file will be calculated using the kmer counts in this k-mer countgraph." />
+    </xml>
+    <xml name="abundance-histogram-output">
+        <data name="output_histogram_filename" format="txt"
+            label="${tool.name} k-mer abundance histogram. The
+                columns are: (1) k-mer abundance, (2) k-mer count, (3)
+                cumulative count, (4) fraction of total distinct k-mers." />
+    </xml>
+    <xml name="output_sequences">
+        <data name="output" format_source="inputs"
+            label="${tool.name} processed nucleotide sequence file">
+            <discover_datasets pattern="__designation_and_ext__" directory="output" visible="true"/>
+        </data>
+    </xml>
+    <xml name="output_sequences_single">
+        <data name="output" format_source="input_sequence_filename"
+            label="${tool.name} processed nucleotide sequence file" />
+    </xml>
+    <xml name="input_zero">
+        <param name="zero" type="boolean" truevalue="" falsevalue="--no-zero" checked="true"
+            help="Output zero count bins (--no-zero)" />
+    </xml>
+    <xml name="input_bigcount">
+        <param  name="bigcount" type="boolean" truevalue="" falsevalue="--no-bigcount"
+            checked="true" help="Count k-mers past 255 occurences (--no-bigcount)" />
+    </xml>
+    <token name="@HELP_FOOTER@"><![CDATA[
+(from the khmer project: http://khmer.readthedocs.org/en/v@WRAPPER_VERSION@/ )]]></token>
+    <xml name="software-citation">
+        <citation type="bibtex">@article{khmer2015,
+     author = "Crusoe, Michael R. and Alameldin, Hussien F. and Awad, Sherine
+  and Bucher, Elmar and Caldwell, Adam and Cartwright, Reed and Charbonneau,
+  Amanda and Constantinides, Bede and Edvenson, Greg and Fay, Scott and Fenton,
+  Jacob and Fenzl, Thomas and Fish, Jordan and Garcia-Gutierrez, Leonor and
+  Garland, Phillip and Gluck, Jonathan and González, Iván and Guermond, Sarah
+  and Guo, Jiarong and Gupta, Aditi and Herr, Joshua R. and Howe, Adina and
+  Hyer, Alex and Härpfer, Andreas and Irber, Luiz and Kidd, Rhys and Lin, David
+  and Lippi, Justin and Mansour, Tamer and McA'Nulty, Pamela and McDonald, Eric
+  and Mizzi, Jessica and Murray, Kevin D. and Nahum, Joshua R. and Nanlohy,
+  Kaben and Nederbragt, Alexander Johan and Ortiz-Zuazaga, Humberto and Ory,
+  Jeramia and Pell, Jason and Pepe-Ranney, Charles and Russ, Zachary N and
+  Schwarz, Erich and Scott, Camille and Seaman, Josiah and Sievert, Scott and
+  Simpson, Jared and Skennerton, Connor T. and Spencer, James and Srinivasan,
+  Ramakrishnan and Standage, Daniel and Stapleton, James A. and Stein, Joe and
+  Steinman, Susan R and Taylor, Benjamin and Trimble, Will and Wiencko, Heather
+  L. and Wright, Michael and Wyss, Brian and Zhang, Qingpeng and zyme, en and
+  Brown, C. Titus"
+     title = "The khmer software package: enabling efficient nucleotide
+  sequence analysis",
+     year = "2015",
+     month = "08",
+     publisher = "F1000",
+     url = "http://dx.doi.org/10.12688/f1000research.6924.1"
+  }</citation>
+    </xml>
+    <xml name="diginorm-citation">
+        <citation type="bibtex">@unpublished{diginorm,
+    author = "Brown, C Titus and Howe, Adina and Zhang, Qingpeng and Pyrkosz,
+Alexis B and Brom, Timothy H",
+    title = "A Reference-Free Algorithm for Computational Normalization of
+Shotgun Sequencing Data",
+    year = "2012",
+    eprint = "arXiv:1203.4802",
+    url = "http://arxiv.org/abs/1203.4802",
+}</citation></xml>
+    <xml name="graph-citation">
+        <citation type="bibtex">@article{Pell2012,
+  doi = {10.1073/pnas.1121464109},
+  url = {http://dx.doi.org/10.1073/pnas.1121464109},
+  year  = {2012},
+  month = {jul},
+  publisher = {Proceedings of the National Academy of Sciences},
+  volume = {109},
+  number = {33},
+  pages = {13272--13277},
+  author = {J. Pell and A. Hintze and R. Canino-Koning and A. Howe and J. M. Tiedje and C. T. Brown},
+  title = {Scaling metagenome sequence assembly with probabilistic de Bruijn graphs},
+  journal = {Proceedings of the National Academy of Sciences}
+  }</citation>
+    </xml>
+    <xml name="counting-citation">
+        <citation type="doi">10.1371/journal.pone.0101271</citation>
+    </xml>
+</macros>