Mercurial > repos > iuc > megan_daa2info

changeset 0:2f8df8e575f2 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
author iuc
date Fri, 03 Dec 2021 23:09:26 +0000
parents
children 9cb0534a9829
files daa2info.xml macros.xml test-data/13-1941-6_S4_L001_R1_600000.fastq.gz test-data/13-1941-6_S4_L001_R2_600000.fastq.gz test-data/blast_R1.txt test-data/blast_R2.txt test-data/contaminants.txt test-data/daa2info_output1.txt test-data/daa2info_output2.txt test-data/daa2info_output_summary2.txt test-data/input.daa test-data/input_meganized.daa test-data/kegg_output.txt test-data/read_extractor_input.rma6 test-data/read_extractor_output.txt test-data/taxonomy_output.txt
diffstat 16 files changed, 1318 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/daa2info.xml	Fri Dec 03 23:09:26 2021 +0000
@@ -0,0 +1,143 @@
+<tool id="megan_daa2info" name="MEGAN: Get information" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>about a DIAMOND file</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="bio_tools"/>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+#set input_identifier = 'input.' + $input.ext.upper()
+ln -s '${input}' '${input_identifier}' &&
+
+daa2info 
+--in '${input_identifier}'
+#if str($input_is_meganized_cond.input_is_meganized) == 'yes':
+    --listMore
+    #if str($input_is_meganized_cond.list_class2count_cond.list_class2count) == 'yes':
+        --class2count '$input_is_meganized_cond.list_class2count_cond.class2count'
+        $input_is_meganized_cond.list_class2count_cond.sum
+    #end if
+    #if str($input_is_meganized_cond.list_read2class_cond.list_read2class) == 'yes':
+        --read2class '$input_is_meganized_cond.list_read2class_cond.read2class'
+    #end if
+    $input_is_meganized_cond.names
+    $input_is_meganized_cond.paths
+    $input_is_meganized_cond.prefixRank
+    $input_is_meganized_cond.majorRanksOnly
+    #if str($input_is_meganized_cond.bo_or_vo) != 'do_not_restrict':
+        $input_is_meganized_cond.bo_or_vo
+    #end if
+    $input_is_meganized_cond.ignoreUnassigned
+#else:
+    --list
+#end if
+#if $extractSummaryFile:
+    --extractSummaryFile '$output_summary'
+#end if
+--out '${output}'
+]]></command>
+    <inputs>
+        <param name="input" argument="--in" type="data" format="daa" label="Input DIAMOND file"/>
+        <conditional name="input_is_meganized_cond">
+            <param name="input_is_meganized" type="select" checked="false" label="Input is meganized?" help="Implies the input file was produced by the MEGAN: DAA Meganizer tool">
+                <option value="no" selected="true">No</option>
+                <option value="yes">Yes</option>
+            </param>
+            <when value="no"/>
+            <when value="yes">
+                <conditional name="list_class2count_cond">
+                    <param name="list_class2count" type="select" label="List class to count for named classification(s)?">
+                        <option value="no" selected="true">No</option>
+                        <option value="yes">Yes</option>
+                    </param>
+                    <when value="no"/>
+                    <when value="yes">
+                        <param argument="--class2count" type="select" label="Select class to count for named classification(s)">
+                            <expand macro="classification_options"/>
+                        </param>
+                        <param argument="--sum" type="boolean" truevalue="--sum" falsevalue="" checked="false" label="Use summarized rather than assigned counts when listing class to count?"/>
+                    </when>
+                </conditional>
+                <conditional name="list_read2class_cond">
+                    <param name="list_read2class" type="boolean" truevalue="true" falsevalue="false" checked="false" label="List read to class assignments for named classification(s)?"/>
+                    <when value="false"/>
+                    <when value="true">
+                        <param argument="--read2class" type="select" label="Select read to class assignments for named classification(s)">
+                            <expand macro="classification_options"/>
+                        </param>
+                    </when>
+                </conditional>
+                <param argument="--names" type="boolean" truevalue="--names" falsevalue="" checked="false" label="Report class names rather than class Id numbers?"/>
+                <param argument="--paths" type="boolean" truevalue="--paths" falsevalue="" checked="false" label="Report class paths rather than class Id numbers?"/>
+                <param argument="--prefixRank" type="boolean" truevalue="--prefixRank" falsevalue="" checked="false" label="When reporting class paths for taxonomy, prefix single letter to indicate taxonomic rank?"/>
+                <param argument="--majorRanksOnly" type="boolean" truevalue="--majorRanksOnly" falsevalue="" checked="false" label="Only use major taxonomic ranks?"/>
+                <param name="bo_or_vo" type="select" label="Restrict reporting to either bacterial reads or viral reads in taxonomic report">
+                    <option value="do_not_restrict" selected="true">Do not restrict</option>
+                    <option value="--bacteriaOnly" selected="true">Bacterial reads and counts</option>
+                    <option value="--virusOnly">Viral reads and counts</option>
+                </param>
+                <param argument="--ignoreUnassigned" type="boolean" truevalue="--ignoreUnassigned" falsevalue="" checked="true" label="Don't report on reads that are unassigned?"/>
+            </when>
+        </conditional>
+        <param argument="--extractSummaryFile" type="boolean" truevalue="--extractSummaryFile" falsevalue="" checked="false" label="Output a MEGAN summary file?" help="Contains all classifications, but no reads or alignments"/>
+    </inputs>
+    <outputs>
+        <data name="output" format="txt"/>
+        <data name="output_summary" format="txt" label="${tool.name} on ${on_string} (MEGAN summary)">
+            <filter>extractSummaryFile</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="input" value="input.daa" ftype="daa"/>
+            <output name="output" file="daa2info_output1.txt" ftype="txt" compare="contains"/>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="input" value="input_meganized.daa" ftype="daa"/>
+            <param name="input_is_meganized" value="yes"/>
+            <output name="output" file="daa2info_output2.txt" ftype="txt" compare="contains"/>
+        </test>
+        <test expect_num_outputs="2">
+            <param name="input" value="input_meganized.daa" ftype="daa"/>
+            <param name="input_is_meganized" value="yes"/>
+            <param name="bo_or_vo" value="--virusOnly"/>
+            <param name="extractSummaryFile" value="true"/>
+            <output name="output" file="daa2info_output2.txt" ftype="txt" compare="contains"/>
+            <output name="output_summary" file="daa2info_output_summary2.txt" ftype="txt" compare="contains"/>
+        </test>
+    </tests>
+    <help>
+**What it does**
+
+Analyses a DIAMOND (i.e., a Direct Access Archive or DAA) file, a proprietary file format developed by PowerISO Computing
+for disk image files, and outputs a text file containing information about the file.  The information includes the following.
+
+ * Number of reads
+ * Alignment mode
+ * Whether the file is meganized
+ * Classifications
+
+If the DIAMOND file is meganized (i.e., it was produced by the MEGAN: DAA Meganizer tool), a summary that includes the
+following information (among other items) is included in the output.
+
+ * Content type
+ * Names
+ * Uids
+ * Sizes
+ * Additional reads
+ * Algorithm
+ * Parameters
+
+If the user elects to output a MEGAN summary file, an additional text file that includes the following information (among
+other items) is produced.
+
+ * Creator
+ * Creation date
+ * Content type
+ * Blast mode
+ * Uids
+
+    </help>
+    <expand macro="citations"/>
+</tool>
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Fri Dec 03 23:09:26 2021 +0000
@@ -0,0 +1,115 @@
+<macros>
+    <token name="@TOOL_VERSION@">6.21.7</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@PROFILE@">20.09</token>
+    <xml name="bio_tools">
+        <xrefs>
+            <xref type="bio.tools">megan</xref>
+        </xrefs>
+    </xml>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">megan</requirement>
+        </requirements>
+    </xml>
+    <macro name="input_type_cond">
+        <conditional name="input_type_cond">
+            <param name="input_type" type="select" label="Choose the category of the reads files to be analyzed">
+                <option value="single" selected="true">Single dataset</option>
+                <option value="pair">Dataset pair</option>
+                <option value="paired">List of dataset pairs</option>
+            </param>
+            <when value="single">
+                <param name="read1" type="data" format="fasta,fasta.gz,fastqsanger.gz,fastqsanger" label="Forward read file" help="This read file should be the one used by Blast to generate the Blast file below"/>
+                <param name="blast1" type="data" format="daa,blastxml,sam,tabular,txt" label="Output file of Blast on input forward read file"/>
+            </when>
+            <when value="pair">
+                <param name="read1" type="data" format="fasta,fasta.gz,fastqsanger.gz,fastqsanger" label="Forward read file" help="This read file should be the one used by Blast to generate the Blast file below"/>
+                <param name="read2" type="data" format="fasta,fasta.gz,fastqsanger.gz,fastqsanger" label="Reverse read file" help="This read file should be the one used by Blast to generate the Blast file below"/>
+                <param argument="--pairedSuffixLength" type="integer" value="0" label="Length of name suffix used to distinguish read names" help="Use 0 if read and mate have the same name"/>
+                <param name="blast1" type="data" format="daa,blastxml,sam,tabular,txt" label="Output file of Blast on input forward read file"/>
+                <param name="blast2" type="data" format="daa,blastxml,sam,tabular,txt" label="Output file of Blast on input reverse read file"/>
+            </when>
+            <when value="paired">
+                <param name="reads_collection" type="data_collection" format="fasta,fasta.gz,fastqsanger,fastqsanger.gz" collection_type="paired" label="Collection of paired read files"/>
+                <param argument="--pairedSuffixLength" type="integer" value="0" label="Length of name suffix used to distinguish read names" help="Use 0 if read and mate have the same name"/>
+                <param name="blast1" type="data" format="daa,blastxml,sam,tabular,txt" label="Blast file for forward read"/>
+                <param name="blast2" type="data" format="daa,blastxml,sam,tabular,txt" label="Blast file for reverse read"/>
+            </when>
+        </conditional>
+    </macro>
+    <macro name="long_reads_param">
+        <param argument="--longReads" type="boolean" truevalue="--longReads" falsevalue="" checked="false" label="Parse and analyse input reads as long reads?"/>
+    </macro>
+    <macro name="classification_options">
+        <option value="EC" selected="true">EC</option>
+        <option value="EGGNOG">EGGNOG</option>
+        <option value="GTDB">GTDB</option>
+        <option value="INTERPRO2GO">INTERPRO2GO</option>
+        <option value="KEGG">KEGG</option>
+        <option value="SEED">SEED</option>
+        <option value="Taxonomy">Taxonomy</option>
+    </macro>
+    <macro name="blast_mode_options">
+        <option value="Unknown" selected="true">Unknown</option>
+        <option value="BlastN">BlastN</option>
+        <option value="BlastP">BlastP</option>
+        <option value="BlastX">BlastX</option>
+        <option value="Classifier">Classifier</option>
+    </macro>
+    <macro name="classify_param">
+        <param argument="--classify" type="boolean" truevalue="--classify" falsevalue="" checked="true" label="Run classification algorithm?"/>
+    </macro>
+    <macro name="blast_params">
+        <param argument="--minScore" type="float" value="50.0" label="Minimum score"/>
+        <param argument="--maxExpected" type="float" value="0.01" label="Maximum expected"/>
+        <param argument="--minPercentIdentity" type="float" value="0.0" min="0.0" max="100.0" label="Minimum percent identity"/>
+        <param argument="--topPercent" type="float" value="10.0" min="0.0" max="100.0" label="Top percent"/>
+    </macro>
+    <macro name="min_max_params">
+        <param argument="--minSupportPercent" type="float" value="0.05" min="0.0" max="100.0" label="Minimum support as percent of assigned reads" help="0 value ignores"/>
+        <param argument="--minSupport" type="integer" value="0" label="Minimum support" help="0 value ignores"/>
+        <param argument="--minPercentReadCover" type="float" value="0.0" min="0.0" max="100.0" label="Minimum percent of read length to be covered by alignments"/>
+        <param argument="--minPercentReferenceCover" type="float" value="0.0" min="0.0" max="100.0" label="Minimum percent of reference length to be covered by alignments"/>
+        <param argument="--minReadLength" type="integer" value="0" label="Minimum read length"/>
+    </macro>
+    <macro name="lca_params">
+        <param argument="--lcaAlgorithm" type="select" label="Select the LCA algorithm to use for taxonomic assignment">
+            <option value="naive" selected="true">naive</option>
+            <option value="weighted">weighted</option>
+            <option value="longReads">longReads</option>
+        </param>
+        <param argument="--lcaCoveragePercent" type="float" value="100.0" min="0.0" max="100.0" label="Percent for the LCA to cover"/>
+    </macro>
+    <macro name="read_assignment_mode_param">
+        <param argument="--readAssignmentMode" type="select" label="Select the read assignment mode">
+            <option value="alignedBases" selected="true">alignedBases</option>
+            <option value="readCount">readCount</option>
+        </param>
+    </macro>
+    <macro name="con_file_param">
+        <param argument="--conFile" type="data" format="txt" optional="true" label="File of contaminant taxa (one id or name per line)" help="Optional, no selection ignores"/>
+    </macro>
+    <macro name="mapdb_param">
+        <param argument="--mapDB" type="data" format="sqlite" optional="true" label="MEGAN mapping db" help="Optional, no selection ignores"/>
+    </macro>
+    <xml name="sanitize_query" token_validinitial="string.printable">
+        <sanitizer>
+            <valid initial="@VALIDINITIAL@">
+                <remove value="&apos;" />
+                <add value="|" />
+            </valid>
+            <mapping initial="none">
+                <add source="&apos;" target="&apos;&quot;&apos;&quot;&apos;" />
+            </mapping>
+       </sanitizer>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1038/nmeth.3176</citation>
+            <citation type="doi">10.1101/gr.120618.111</citation>
+            <citation type="doi">10.1101/gr.5969107</citation>
+        </citations>
+    </xml>
+</macros>
+
Binary file test-data/13-1941-6_S4_L001_R1_600000.fastq.gz has changed
Binary file test-data/13-1941-6_S4_L001_R2_600000.fastq.gz has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/blast_R1.txt	Fri Dec 03 23:09:26 2021 +0000
@@ -0,0 +1,404 @@
+BLASTN output produced by MALT
+
+
+Query= XXXXXXXXXX:7:1101:1582:1835#/1
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+***** No hits found ******
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+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:2269:1904#/1
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:3444:100163#/1
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:2259:1943#/1
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:3371:100179#/1
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:2371:1957#/1
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:3311:100186#/1
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:2394:1961#/1
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:3438:100192#/1
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:2333:1962#/1
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:3479:100209#/1
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:2459:1990#/1
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:3417:100210#/1
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:2372:1994#/1
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:3452:100214#/1
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:2677:1830#/1
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:3354:100219#/1
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:2603:1846#/1
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:3600:100019#/1
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:2535:1848#/1
+
+***** No hits found ******
+
+EOF
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/blast_R2.txt	Fri Dec 03 23:09:26 2021 +0000
@@ -0,0 +1,404 @@
+BLASTN output produced by MALT
+
+
+Query= XXXXXXXXXX:7:1101:1582:1835#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:1610:1859#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:1743:1871#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:1536:1878#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:2990:100153#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:1624:1906#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:1666:1926#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:2921:100163#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:1513:1929#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:2759:100170#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:1708:1937#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:2981:100211#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:1688:1946#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:2767:100225#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:1536:1959#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:2797:100234#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:1552:1976#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:1748:1978#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:2779:100239#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:1593:1980#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:2946:100242#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:1987:1781#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:3046:100006#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:1900:1788#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:3214:100027#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:1848:1879#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:3237:100032#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:3027:100049#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:1756:1891#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:3238:100065#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:1915:1901#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:3198:100082#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:1964:1931#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:3088:100091#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:1840:1948#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:3105:100094#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:1958:1952#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:3190:100106#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:1993:1999#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:3117:100110#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:2159:1798#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:3147:100111#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:2152:1838#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:3065:100152#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:2180:1843#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:3154:100159#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:2125:1861#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:3198:100173#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:2076:1911#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:3166:100190#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:2196:1920#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:3225:100207#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:2115:1927#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:3019:100219#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:2179:1937#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:3202:100230#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:2149:1945#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:3211:100242#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:2169:1964#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:3168:100244#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:3005:100246#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:2313:1789#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:3253:100014#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:2361:1794#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:2337:1794#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:3284:100039#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:2477:1795#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:3310:100056#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:2355:1821#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:3420:100060#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:2418:1834#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:3267:100061#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:2378:1838#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:3416:100083#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:2481:1853#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:3411:100111#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:3258:100128#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:2252:1856#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:3428:100129#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:2394:1871#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:3387:100138#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:2269:1904#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:3444:100163#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:2259:1943#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:3371:100179#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:2371:1957#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:3311:100186#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:2394:1961#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:3438:100192#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:2333:1962#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:3479:100209#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:2459:1990#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:3417:100210#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:2372:1994#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:3452:100214#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:2677:1830#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:3354:100219#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:2603:1846#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:3600:100019#/2
+
+***** No hits found ******
+
+Query= XXXXXXXXXX:7:1101:2535:1848#/2
+
+***** No hits found ******
+
+EOF
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/contaminants.txt	Fri Dec 03 23:09:26 2021 +0000
@@ -0,0 +1,12 @@
+Illumina Single End Adapter 1					ACACTCTTTCCCTACACGACGCTGTTCCATCT
+Illumina Single End Adapter 2					CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT
+Illumina Single End PCR Primer 1				AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
+Illumina Single End PCR Primer 2				CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT
+Illumina Single End Sequencing Primer			ACACTCTTTCCCTACACGACGCTCTTCCGATCT
+
+Illumina Paired End Adapter 1					ACACTCTTTCCCTACACGACGCTCTTCCGATCT
+Illumina Paired End Adapter 2					CTCGGCATTCCTGCTGAACCGCTCTTCCGATCT
+Illumina Paried End PCR Primer 1				AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
+Illumina Paired End PCR Primer 2				CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT
+Illumina Paried End Sequencing Primer 1			ACACTCTTTCCCTACACGACGCTCTTCCGATCT
+Illumina Paired End Sequencing Primer 2			CGGTCTCGGCATTCCTACTGAACCGCTCTTCCGATCT
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/daa2info_output1.txt	Fri Dec 03 23:09:26 2021 +0000
@@ -0,0 +1,3 @@
+# Number of reads: 1
+# Alignment mode:  BLASTP
+# Is meganized:    false
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/daa2info_output2.txt	Fri Dec 03 23:09:26 2021 +0000
@@ -0,0 +1,19 @@
+# Number of reads: 1
+# Alignment mode:  BLASTP
+# Is meganized:    true
+# Classifications: Taxonomy
+# Meganization summary:
+## @Creator	DAA2Info
+## @CreationDate
+## @ContentType	Summary4
+## @Names	input
+## @BlastMode	BlastP
+## @Uids
+## @Sizes	1.0
+## @TotalReads	1
+## @AdditionalReads	0
+## Classifications:
+##  Taxonomy (1 classes)
+## @Algorithm	Taxonomy	merge
+## @Parameters	
+## 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/daa2info_output_summary2.txt	Fri Dec 03 23:09:26 2021 +0000
@@ -0,0 +1,16 @@
+@Creator	DAA2Info
+@CreationDate
+@ContentType	Summary4
+@Names	input
+@BlastMode	BlastP
+@Uids
+@Sizes	1
+@TotalReads	1
+@AdditionalReads	0
+@Algorithm	Taxonomy	merge
+@Parameters	
+@ColorTable	Fews8	White-Green
+TAX	-2	1
+END_OF_DATA_TABLE
+#SampleID	@Source
+input.daa	input.DAA
Binary file test-data/input.daa has changed
Binary file test-data/input_meganized.daa has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/kegg_output.txt	Fri Dec 03 23:09:26 2021 +0000
@@ -0,0 +1,100 @@
+XXXXXXXXXX:7:1101:1582:1835#/1; ;
+XXXXXXXXXX:7:1101:1610:1859#/1; ;
+XXXXXXXXXX:7:1101:1743:1871#/1; ;
+XXXXXXXXXX:7:1101:1536:1878#/1; ;
+XXXXXXXXXX:7:1101:2990:100153#/1; ;
+XXXXXXXXXX:7:1101:1624:1906#/1; ;
+XXXXXXXXXX:7:1101:1666:1926#/1; ;
+XXXXXXXXXX:7:1101:2921:100163#/1; ;
+XXXXXXXXXX:7:1101:1513:1929#/1; ;
+XXXXXXXXXX:7:1101:2759:100170#/1; ;
+XXXXXXXXXX:7:1101:1708:1937#/1; ;
+XXXXXXXXXX:7:1101:2981:100211#/1; ;
+XXXXXXXXXX:7:1101:1688:1946#/1; ;
+XXXXXXXXXX:7:1101:2767:100225#/1; ;
+XXXXXXXXXX:7:1101:1536:1959#/1; ;
+XXXXXXXXXX:7:1101:2797:100234#/1; ;
+XXXXXXXXXX:7:1101:1552:1976#/1; ;
+XXXXXXXXXX:7:1101:1748:1978#/1; ;
+XXXXXXXXXX:7:1101:2779:100239#/1; ;
+XXXXXXXXXX:7:1101:1593:1980#/1; ;
+XXXXXXXXXX:7:1101:2946:100242#/1; ;
+XXXXXXXXXX:7:1101:1987:1781#/1; ;
+XXXXXXXXXX:7:1101:3046:100006#/1; ;
+XXXXXXXXXX:7:1101:1900:1788#/1; ;
+XXXXXXXXXX:7:1101:3214:100027#/1; ;
+XXXXXXXXXX:7:1101:1848:1879#/1; ;
+XXXXXXXXXX:7:1101:3237:100032#/1; ;
+XXXXXXXXXX:7:1101:3027:100049#/1; ;
+XXXXXXXXXX:7:1101:1756:1891#/1; ;
+XXXXXXXXXX:7:1101:3238:100065#/1; ;
+XXXXXXXXXX:7:1101:1915:1901#/1; ;
+XXXXXXXXXX:7:1101:3198:100082#/1; ;
+XXXXXXXXXX:7:1101:1964:1931#/1; ;
+XXXXXXXXXX:7:1101:3088:100091#/1; ;
+XXXXXXXXXX:7:1101:1840:1948#/1; ;
+XXXXXXXXXX:7:1101:3105:100094#/1; ;
+XXXXXXXXXX:7:1101:1958:1952#/1; ;
+XXXXXXXXXX:7:1101:3190:100106#/1; ;
+XXXXXXXXXX:7:1101:1993:1999#/1; ;
+XXXXXXXXXX:7:1101:3117:100110#/1; ;
+XXXXXXXXXX:7:1101:2159:1798#/1; ;
+XXXXXXXXXX:7:1101:3147:100111#/1; ;
+XXXXXXXXXX:7:1101:2152:1838#/1; ;
+XXXXXXXXXX:7:1101:3065:100152#/1; ;
+XXXXXXXXXX:7:1101:2180:1843#/1; ;
+XXXXXXXXXX:7:1101:3154:100159#/1; ;
+XXXXXXXXXX:7:1101:2125:1861#/1; ;
+XXXXXXXXXX:7:1101:3198:100173#/1; ;
+XXXXXXXXXX:7:1101:2076:1911#/1; ;
+XXXXXXXXXX:7:1101:3166:100190#/1; ;
+XXXXXXXXXX:7:1101:2196:1920#/1; ;
+XXXXXXXXXX:7:1101:3225:100207#/1; ;
+XXXXXXXXXX:7:1101:2115:1927#/1; ;
+XXXXXXXXXX:7:1101:3019:100219#/1; ;
+XXXXXXXXXX:7:1101:2179:1937#/1; ;
+XXXXXXXXXX:7:1101:3202:100230#/1; ;
+XXXXXXXXXX:7:1101:2149:1945#/1; ;
+XXXXXXXXXX:7:1101:3211:100242#/1; ;
+XXXXXXXXXX:7:1101:2169:1964#/1; ;
+XXXXXXXXXX:7:1101:3168:100244#/1; ;
+XXXXXXXXXX:7:1101:3005:100246#/1; ;
+XXXXXXXXXX:7:1101:2313:1789#/1; ;
+XXXXXXXXXX:7:1101:3253:100014#/1; ;
+XXXXXXXXXX:7:1101:2361:1794#/1; ;
+XXXXXXXXXX:7:1101:2337:1794#/1; ;
+XXXXXXXXXX:7:1101:3284:100039#/1; ;
+XXXXXXXXXX:7:1101:2477:1795#/1; ;
+XXXXXXXXXX:7:1101:3310:100056#/1; ;
+XXXXXXXXXX:7:1101:2355:1821#/1; ;
+XXXXXXXXXX:7:1101:3420:100060#/1; ;
+XXXXXXXXXX:7:1101:2418:1834#/1; ;
+XXXXXXXXXX:7:1101:3267:100061#/1; ;
+XXXXXXXXXX:7:1101:2378:1838#/1; ;
+XXXXXXXXXX:7:1101:3416:100083#/1; ;
+XXXXXXXXXX:7:1101:2481:1853#/1; ;
+XXXXXXXXXX:7:1101:3411:100111#/1; ;
+XXXXXXXXXX:7:1101:3258:100128#/1; ;
+XXXXXXXXXX:7:1101:2252:1856#/1; ;
+XXXXXXXXXX:7:1101:3428:100129#/1; ;
+XXXXXXXXXX:7:1101:2394:1871#/1; ;
+XXXXXXXXXX:7:1101:3387:100138#/1; ;
+XXXXXXXXXX:7:1101:2269:1904#/1; ;
+XXXXXXXXXX:7:1101:3444:100163#/1; ;
+XXXXXXXXXX:7:1101:2259:1943#/1; ;
+XXXXXXXXXX:7:1101:3371:100179#/1; ;
+XXXXXXXXXX:7:1101:2371:1957#/1; ;
+XXXXXXXXXX:7:1101:3311:100186#/1; ;
+XXXXXXXXXX:7:1101:2394:1961#/1; ;
+XXXXXXXXXX:7:1101:3438:100192#/1; ;
+XXXXXXXXXX:7:1101:2333:1962#/1; ;
+XXXXXXXXXX:7:1101:3479:100209#/1; ;
+XXXXXXXXXX:7:1101:2459:1990#/1; ;
+XXXXXXXXXX:7:1101:3417:100210#/1; ;
+XXXXXXXXXX:7:1101:2372:1994#/1; ;
+XXXXXXXXXX:7:1101:3452:100214#/1; ;
+XXXXXXXXXX:7:1101:2677:1830#/1; ;
+XXXXXXXXXX:7:1101:3354:100219#/1; ;
+XXXXXXXXXX:7:1101:2603:1846#/1; ;
+XXXXXXXXXX:7:1101:3600:100019#/1; ;
+XXXXXXXXXX:7:1101:2535:1848#/1; ;
Binary file test-data/read_extractor_input.rma6 has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/read_extractor_output.txt	Fri Dec 03 23:09:26 2021 +0000
@@ -0,0 +1,2 @@
+>sequence
+LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLVEWIWGGFSVDKATLNRFFAFHFILFTMVALAGVHLTFLHETGSNNPLGLTSDSDKIPFHPYYTIKDFLGLXXXXXXXXXXXXXSPDMLGDPDNHMPADPLNTPLHIKPEWYFLFAYAILRSVPNKLGGVLALFLSIVILGLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGXIENY
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/taxonomy_output.txt	Fri Dec 03 23:09:26 2021 +0000
@@ -0,0 +1,100 @@
+XXXXXXXXXX:7:1101:1582:1835#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:1610:1859#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:1743:1871#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:1536:1878#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:2990:100153#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:1624:1906#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:1666:1926#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:2921:100163#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:1513:1929#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:2759:100170#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:1708:1937#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:2981:100211#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:1688:1946#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:2767:100225#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:1536:1959#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:2797:100234#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:1552:1976#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:1748:1978#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:2779:100239#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:1593:1980#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:2946:100242#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:1987:1781#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:3046:100006#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:1900:1788#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:3214:100027#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:1848:1879#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:3237:100032#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:3027:100049#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:1756:1891#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:3238:100065#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:1915:1901#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:3198:100082#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:1964:1931#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:3088:100091#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:1840:1948#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:3105:100094#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:1958:1952#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:3190:100106#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:1993:1999#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:3117:100110#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:2159:1798#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:3147:100111#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:2152:1838#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:3065:100152#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:2180:1843#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:3154:100159#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:2125:1861#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:3198:100173#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:2076:1911#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:3166:100190#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:2196:1920#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:3225:100207#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:2115:1927#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:3019:100219#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:2179:1937#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:3202:100230#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:2149:1945#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:3211:100242#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:2169:1964#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:3168:100244#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:3005:100246#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:2313:1789#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:3253:100014#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:2361:1794#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:2337:1794#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:3284:100039#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:2477:1795#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:3310:100056#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:2355:1821#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:3420:100060#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:2418:1834#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:3267:100061#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:2378:1838#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:3416:100083#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:2481:1853#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:3411:100111#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:3258:100128#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:2252:1856#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:3428:100129#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:2394:1871#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:3387:100138#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:2269:1904#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:3444:100163#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:2259:1943#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:3371:100179#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:2371:1957#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:3311:100186#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:2394:1961#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:3438:100192#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:2333:1962#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:3479:100209#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:2459:1990#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:3417:100210#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:2372:1994#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:3452:100214#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:2677:1830#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:3354:100219#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:2603:1846#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:3600:100019#/1; ; No hits; 100;
+XXXXXXXXXX:7:1101:2535:1848#/1; ; No hits; 100;