--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/jellyfish.xml	Mon Apr 12 18:18:53 2021 +0000
@@ -0,0 +1,255 @@
+<tool id="jellyfish" name="jellyfish" version="@WRAPPER_VERSION@+@VERSION_SUFFIX@" profile="20.01">
+    <macros>
+        <token name="@WRAPPER_VERSION@">2.3.0</token>
+        <token name="@VERSION_SUFFIX@">galaxy0</token>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@WRAPPER_VERSION@">kmer-jellyfish</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        jellyfish
+        #if $commands.command == "count":
+            count
+            --mer-len $commands.mer_len
+            --size $commands.size
+            #if $commands.counter_len:
+                --counter-len $commands.counter_len
+            #end if
+            $commands.canonical
+            #if $commands.bloom.filters == "bc":
+                --bc '$commands.bloom.bloom_file'
+                #if $commands.bloom.bf_fp:
+                    --bf-fp $commands.bloom.bf_fp
+                #end if
+            #else if $commands.bloom.filters == "bf_size":
+                --bf-size $commands.bloom.bf_size
+                #if $commands.bloom.bf_fp:
+                    --bf-fp $commands.bloom.bf_fp
+                #end if
+            #end if
+            #if $commands.if:
+                --if '$commands.if'
+            #end if
+            #if $commands.reprobes:
+                --reprobes $commands.reprobes
+            #end if
+            #if $commands.text == "text":
+                --text
+            #end if
+            #if $commands.lower_count:
+                --lower-count $commands.lower_count
+            #end if
+            #if $commands.upper_count:
+                --upper-count $commands.upper_count
+            #end if
+            '$commands.input'
+        #else if $commands.command == "histo":
+            histo
+            #if $commands.low:
+                --low $commands.low
+            #end if
+            #if $commands.high:
+                --high $commands.high
+            #end if
+            #if $commands.increment:
+                --increment $commands.increment
+            #end if
+            $commands.full
+            '$commands.input'
+            -o jellyfish_histo.txt
+        #else if $commands.command == "dump":
+            dump
+            #if $commands.lower_count:
+                --lower-count $commands.lower_count
+            #end if
+            #if $commands.upper_count:
+                --upper-count $commands.upper_count
+            #end if
+            #if $commands.format.format_select == "column":
+                --column
+                $commands.format.tab
+                '$commands.input'
+                #if $commands.format.tab == "--tab":
+                    -o jellyfish_dump.tsv
+                #else:
+                    -o jellyfish_dump.txt
+                #end if
+            #else:
+                '$commands.input'
+                -o jellyfish_dump.fasta
+            #end if
+        ## #else if $commands.command == "bc":
+        ## #else if $commands.command == "info":
+        ## #else if $commands.command == "stats":
+        ## #else if $commands.command == "merge":
+        ## #else if $commands.command == "query":
+        #end if
+    ]]></command>
+    <inputs>
+        <conditional name="commands">
+            <param name="command" type="select" label="Jellyfish command: ">
+                <option value="count"/>
+                <option value="histo"/>
+                <option value="dump"/>
+                <!-- <option value="bc"/>
+                <option value="info"/>
+                <option value="stats"/>
+                <option value="merge"/>
+                <option value="query"/> -->
+            </param>
+            <when value="count">
+                <param name="input" type="data" format="fasta,fastq,fastqsanger" label="Input data file"/>
+                <param argument="--mer-len" type="integer" value="20" min="1" label="Length of mer" />
+                <param argument="--size" type="integer" value="32" min="1" label="Initial hash size" />
+                <param argument="--counter-len" type="integer" min="1" optional="true" label="Counter Length in bits" />
+                <param argument="--canonical" type="boolean" truevalue="--canonical" falsevalue="" label="Count both strand and canonical representation" />
+                <conditional name="bloom">
+                    <param name="filters" type="select" label="Use bloom filters">
+                        <option value="default">Default</option>
+                        <option value="bc">Bloom counter to filter out singleton mers</option>
+                        <option value="bf_size">Use bloom filter to count high-frequency mers</option>
+                    </param>
+                    <when value="default"/>
+                    <when value="bc">
+                        <param name="bloom_file" type="data" format="tabular,tsv" label="Bloom counter file"/>
+                        <param argument="--bf-fp" type="float" label="False positive rate of bloom filter" optional="true"/>
+                    </when>
+                    <when value="bf_size">
+                        <param name="bf_size" argument="--bf-size" type="integer" label="Use bloom filter to count high-frequency mers"  min="1" optional="true"/>
+                        <param argument="--bf-fp" type="float" label="False positive rate of bloom filter" optional="true"/>
+                    </when>
+                </conditional>
+                <param argument="--if" type="data" format="txt" label="Count only k-mers in this file" optional="true"/>
+                <param argument="--reprobes" type="integer" label="Maximum number of repropbes" min="1" optional="true"/>
+                <param argument="--text" type="boolean" label="Dump in text format" truevalue="text" falsevalue="jf"/>
+                <param argument="--lower-count" type="integer" label="Lower count" min="1" optional="true" help="Don't output k-mer with count less than this value"/>
+                <param argument="--upper-count" type="integer" label="upper count" min="1" optional="true" help="Don't output k-mer with count greater than this value"/>
+            </when>
+            <when value="histo"> 
+                <param name="input" type="data" format="jellyfish" label="Input data file"/>
+                <param argument="--low" type="integer" min="1" label="Lower count value of histogram" optional="true"/>
+                <param argument="--high" type="integer" min="1" label="Upper count value of histogram" optional="true"/>
+                <param argument="--increment" type="integer" min="1" label="Increment value for buckets" optional="true"/>
+                <param argument="--full" type="boolean" label="Full histogram. Don't skip count 0" truevalue="--full" falsevalue=""/>
+            </when>
+            <when value="dump"> 
+                <param name="input" type="data" format="jellyfish" label="Input data file"/>
+                <conditional name="format">
+                    <param name="format_select" type="select" label="Output format">
+                        <option value="fasta"/>
+                        <option value="column"/>
+                    </param>
+                    <when value="fasta"/>
+                    <when value="column">
+                        <param argument="--tab" type="boolean" label="Use tab separator" truevalue="--tab" falsevalue=""/>
+                    </when>
+                </conditional>
+                <param argument="--lower-count" type="integer" min="0" optional="true" label="Don't output k-mer with count less than lower-count" />
+                <param argument="--upper-count" type="integer" min="1" optional="true" label="Don't output k-mer with count greater than upper-count" />
+            </when>
+            <!-- <when value="bc"> 
+            </when>
+            <when value="info"> 
+
+            </when>
+            <when value="stats"> 
+
+            </when>
+            <when value="merge"> 
+
+            </when>
+            <when value="query"> 
+
+            </when> -->
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="jellyfish_db" format="jellyfish" from_work_dir="mer_counts.jf" label="${tool.name} on ${on_string}: jellyfish db">
+            <filter>commands["command"] == "count" and not commands["text"]</filter>
+        </data>
+        <data name="jellyfish_db_txt" format="txt" from_work_dir="mer_counts.jf" label="${tool.name} on ${on_string}: jellyfish db text">
+            <filter>commands["command"] == "count" and commands["text"]</filter>
+        </data>
+        <data name="jellyfish_histo" format="txt" from_work_dir="jellyfish_histo.txt" label="${tool.name} on ${on_string}: histogram">
+            <filter>commands["command"] == "histo"</filter>
+        </data>
+        <data name="jellyfish_fasta" format="fasta" from_work_dir="jellyfish_dump.fasta" label="${tool.name} on ${on_string}: fasta dump">
+            <filter>commands["command"] == "dump" and commands["format"]["format_select"] == "fasta"</filter>
+        </data>
+        <data name="jellyfish_txt" format="txt" from_work_dir="jellyfish_dump.txt" label="${tool.name} on ${on_string}: txt dump">
+            <filter>commands["command"] == "dump" and commands["format"]["format_select"] == "column" and not commands["format"]["tab"]</filter>
+        </data>
+        <data name="jellyfish_tsv" format="tsv" from_work_dir="jellyfish_dump.tsv" label="${tool.name} on ${on_string}: tabular dump">
+            <filter>commands["command"] == "dump" and commands["format"]["format_select"] == "column" and commands["format"]["tab"]</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <conditional name="commands">
+                <param name="commands" value="count"/>
+                <param name="input" value="test.fastq"/>
+                <param name="mer_len" value="22"/>
+                <param name="size" value="16"/>
+                <param name="canonical" value="--canonical"/>
+            </conditional>
+            <output name="jellyfish_db" file="out.jf" compare="sim_size" delta="1000"/>
+        </test>
+        <test expect_num_outputs="1">
+            <conditional name="commands">
+                <param name="commands" value="count"/>
+                <param name="input" value="test.fastq"/>
+                <param name="mer_len" value="22"/>
+                <param name="size" value="16"/>
+                <param name="canonical" value="--canonical"/>
+                <conditional name="bloom">
+                    <param name="filters" value="bf_size"/>
+                    <param name="bf_size" value="2"/>
+                    <param name="bf_fp" value="0.01"/>
+                </conditional>
+                <param name="text" value="text"/>
+                <param name="lower" value="1"/>
+                <param name="upper" value="20"/>
+            </conditional>
+            <output name="jellyfish_db_txt" file="out.jf.txt" lines_diff="2"/>
+        </test>
+        <test expect_num_outputs="1">
+            <conditional name="commands">
+                <param name="command" value="histo"/>
+                <param name="input" value="out.jf"/>
+                <param name="low" value="1"/>
+                <param name="high" value="10000"/>
+                <param name="full" value="--full"/> 
+                <param name="increment" value="100"/>
+            </conditional>
+            <output name="jellyfish_histo" ftype="txt" file="histo.txt"/>
+        </test>
+        <test expect_num_outputs="1">
+            <conditional name="commands">
+                <param name="command" value="dump"/>
+                <param name="input" value="out.jf"/>
+                <param name="lower_count" value="3"/>
+            </conditional>
+            <output name="jellyfish_fasta" ftype="fasta" file="dump.fasta"/>
+        </test>
+        <test expect_num_outputs="1">
+            <conditional name="commands">
+                <param name="command" value="dump"/>
+                <param name="input" value="out.jf"/>
+                <conditional name="format">
+                    <param name="format_select" value="column"/>
+                    <param name="tab" value="--tab"/>
+                </conditional>
+                <param name="upper_count" value="100"/>
+            </conditional>
+            <output name="jellyfish_tsv" ftype="tsv" file="dump.tsv"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+        Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence. Jellyfish can count k-mers using an order of magnitude less memory and an order of magnitude faster than other k-mer counting packages by using an efficient encoding of a hash table and by exploiting the "compare-and-swap" CPU instruction to increase parallelism.
+
+        JELLYFISH is a command-line program that reads FASTA and multi-FASTA files containing DNA sequences. It outputs its k-mer counts in a binary format, which can be translated into a human-readable text format using the "jellyfish dump" command, or queried for specific k-mers with "jellyfish query". See the documentation for details.
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/btr011</citation>
+    </citations>
+</tool>