Repository 'metabat2'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/metabat2

Changeset 0:76bc4efa1aeb (2022-01-28)
Next changeset 1:01f02c5ddff8 (2022-07-29)
Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit 4baddc43c4fdbe9fa7fe056bc3f9213de01516dd"
added:
macros.xml
metabat2.xml
test-data/NC_002945v4.fasta
test-data/fasta_indexes.loc
test-data/input0.fasta.gz
test-data/input1.bam
test-data/input2.bam
test-data/input_depth1.tabular
test-data/jgi_output1.tabular
test-data/jgi_output2.tabular
test-data/jgi_output_depth1.tabular
test-data/jgi_output_gc1.tabular
test-data/jgi_output_kmers1.tabular
test-data/jgi_output_paired_contigs1.fasta
test-data/jgi_output_read_stats1.tabular
test-data/process_log.txt
tool-data/fasta_indexes.loc.sample
tool_data_table_conf.xml.sample
tool_data_table_conf.xml.test
b
diff -r 000000000000 -r 76bc4efa1aeb macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Fri Jan 28 12:21:05 2022 +0000
b
@@ -0,0 +1,15 @@
+<macros>
+    <token name="@TOOL_VERSION@">2.15</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@PROFILE@">21.01</token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">metabat2</requirement>
+        </requirements>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.7717/peerj.7359</citation>
+        </citations>
+    </xml>
+</macros>
b
diff -r 000000000000 -r 76bc4efa1aeb metabat2.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/metabat2.xml Fri Jan 28 12:21:05 2022 +0000
[
@@ -0,0 +1,131 @@
+<tool id="metabat2" name="MetaBAT2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>metagenome binning</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+mkdir bins &&
+metabat2
+--inFile '$inFile'
+--outFile 'bins/bin'
+#if str($advanced.base_coverage_depth_cond.base_coverage_depth) == 'yes':
+    #if $advanced.base_coverage_depth_cond.abdFile:
+        --abdFile '$advanced.base_coverage_depth_cond.abdFile'
+    #else if $advanced.base_coverage_depth_cond.cvExt:
+        --cvExt '$advanced.base_coverage_depth_cond.cvExt'
+    #end if
+#end if
+--minContig $advanced.minContig
+--maxP $advanced.maxP
+--minS $advanced.minS
+--maxEdges $advanced.maxEdges
+--pTNF $advanced.pTNF
+$advanced.noAdd
+--minCV $advanced.minCV
+--minCVSum $advanced.minCVSum
+--minClsSize $advanced.minClsSize
+--numThreads \${GALAXY_SLOTS:-4}
+$advanced.onlyLabel
+#if $advanced.saveCls:
+    $advanced.saveCls
+    --noBinOut
+#end if
+$advanced.unbinned
+--seed $advanced.seed
+> process_log.txt
+#if str($advanced.output_process_log) == 'yes':
+    && mv process_log.txt '$process_log'
+#end if
+    ]]></command>
+    <inputs>
+        <param argument="--inFile" type="data" format="fasta,fasta.gz" label="Fasta file containing contigs"/>
+        <section name="advanced" title="Advanced options">
+            <conditional name="base_coverage_depth_cond">
+                <param name="base_coverage_depth" type="select" label="Use a base coverage depth file?">
+                    <option value="no" selected="true">No</option>
+                    <option value="yes">Yes</option>
+                </param>
+                <when value="no"/>
+                <when value="yes">
+                    <param argument="--abdFile" type="data" format="tabular" optional="True" label="Tabular depth matrix file having mean and variance of base coverage depth" help="Generated by the Calculate contig depths for MetaBAT2 tool"/>
+                    <param argument="--cvExt" type="data" format="tabular" optional="True" label="Base coverage depth file without variance" help="Generated by a tool - not the Calculate contig depths for MetaBAT2 tool"/>
+                </when>
+            </conditional>
+            <param argument="--minContig" type="integer" min="1500" value="1500" label="Minimum size of a contig for binning"/>
+            <param argument="--maxP" type="integer" min="1" max="100" value="95" label="Percentage of good contigs considered for binning decided by connection among contigs" help="The greater, the more sensitive"/>
+            <param argument="--minS" type="integer" min="1" max="99" value="60" label="Minimum score of an edge for binning" help="The greater, the more specific"/>
+            <param argument="--maxEdges" type="integer" value="200" label="Maximum number of edges per node" help="The greater, the more sensitive"/>
+            <param argument="--pTNF" type="integer" value="0" label="TNF probability cutoff for building TNF graph" help="Use it to skip the preparation step (0:auto)"/>
+            <param argument="--noAdd" type="boolean" truevalue="--noAdd" falsevalue="" checked="false" label="Turn off additional binning for lost or small contigs?"/>
+            <param argument="--minCV" type="float" value="1.0" label="Minimum mean coverage of a contig in each library for binning"/>
+            <param argument="--minCVSum" type="float" value="1.0" label="Minimum total effective mean coverage of a contig for binning" help="Sum of depth over minCV"/>
+            <param argument="--minClsSize" type="integer" value="200000" label="Minimum size of a bin as the output"/>
+            <param argument="--onlyLabel" type="boolean" truevalue="--onlyLabel" falsevalue="" checked="false" label="Output only sequence labels as a list in a column without sequences?"/>
+            <param argument="--saveCls" type="boolean" truevalue="--saveCls" falsevalue="" checked="false" label="Save cluster memberships as a matrix format?"/>
+            <param argument="--unbinned" type="boolean" truevalue="--unbinned" falsevalue="" checked="false" label="Output fasta file containing unbinned contigs?"/>
+            <param argument="--seed" type="integer" value="0" label="For exact reproducibility." help="Zero value will use random seed"/>
+            <param name="output_process_log" type="select" label="Output process log file?">
+                <option value="no" selected="true">No</option>
+                <option value="yes">Yes</option>
+            </param>
+        </section>
+    </inputs>
+    <outputs>
+        <collection name="bin_files" type="list" label="${tool.name} on ${on_string}: (bins)">
+            <discover_datasets pattern="(?P&lt;designation&gt;.*)\.fa" format="fasta" directory="bins"/>
+        </collection>
+        <data name="process_log" format="txt" label="${tool.name} on ${on_string} (process log)">
+            <filter>advanced['output_process_log'] == 'yes'</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="inFile" value="input0.fasta.gz" ftype="fasta.gz"/>
+            <param name="seed" value="345678"/>
+            <output_collection name="bin_files" type="list" count="2">
+                <element name="bin.1" ftype="fasta">
+                    <assert_contents>
+                        <has_size value="334554"/>
+                    </assert_contents>
+                </element>
+                <element name="bin.2" ftype="fasta">
+                    <assert_contents>
+                        <has_size value="577866"/>
+                    </assert_contents>
+                </element>
+            </output_collection>
+        </test>
+        <test expect_num_outputs="2">
+            <param name="inFile" value="input0.fasta.gz" ftype="fasta.gz"/>
+            <param name="base_coverage_depth" value="yes"/>
+            <param name="abdFile" value="input_depth1.tabular" ftype="tabular"/>
+            <param name="seed" value="345678"/>
+            <param name="output_process_log" value="yes"/>
+            <output_collection name="bin_files" type="list" count="0"/>
+            <output name="process_log" file="process_log.txt" ftype="txt"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+**What it does**
+
+MetaBAT2 (Metagenome Binning based on Abundance and Tetranucleotide frequency) is an automated metagenome binning
+software that integrates empirical probabilistic distances of genome abundance and tetranucleotide frequency.  The
+tool accepts a fast file containing contigs and produces a collection (i.e., bins) of fasta files.
+        
+MetaBAT2 includes optionizations to MetaBAT.  It requires virtually no parameter optimization. Default parameter
+values are more reliable to use in most cases since MetaBAT2 adapts to the given data to find the best parameter.
+Some parameter settings are still available for advanced users, helping to manage some exceptional cases by changing
+the amount of data used for the analysis.
+
+**More information**
+
+https://bitbucket.org/berkeleylab/metabat/src/master/
+
+**Options**
+
+ * **Use base coverage depth file** - optionally select a base coverage depth file that was either generated by the Calculate contig depths for MetaBAT2 tool or another 3rd party tool.

+    ]]></help>
+    <expand macro="citations"/>
+</tool>
b
diff -r 000000000000 -r 76bc4efa1aeb test-data/NC_002945v4.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/NC_002945v4.fasta Fri Jan 28 12:21:05 2022 +0000
b
@@ -0,0 +1,101 @@
+>NC_002945.4 Mycobacterium bovis AF2122/97 genome assembly, chromosome: Mycobacterium_bovis_AF2122/97
+TTGACCGATGACCCCGGTTCAGGCTTCACCACAGTGTGGAACGCGGTCGTCTCCGAACTTAACGGCGACC
+CTAAGGTTGACGACGGACCCAGCAGTGATGCTAATCTCAGCGCTCCGCTGACCCCTCAGCAAAGGGCTTG
+GCTCAATCTCGTCCAGCCATTGACCATCGTCGAGGGGTTTGCTCTGTTATCCGTGCCGAGCAGCTTTGTC
+CAAAACGAAATCGAGCGCCATCTGCGGGCCCCGATTACCGACGCTCTCAGCCGCCGACTCGGACATCAGA
+TCCAACTCGGGGTCCGCATCGCTCCGCCGGCGACCGACGAAGCCGACGACACTACCGTGCCGCCTTCCGA
+AAATCCTGCTACCACATCGCCAGACACCACAACCGACAACGACGAGATTGATGACAGCGCTGCGGCACGG
+GGCGATAACCAGCACAGTTGGCCAAGTTACTTCACCGAGCGCCCGCGCAATACCGATTCCGCTACCGCTG
+GCGTAACCAGCCTTAACCGTCGCTACACCTTTGATACGTTCGTTATCGGCGCCTCCAACCGGTTCGCGCA
+CGCCGCCGCCTTGGCGATCGCAGAAGCACCCGCCCGCGCTTACAACCCCCTGTTCATCTGGGGCGAGTCC
+GGTCTCGGCAAGACACACCTGCTACACGCGGCAGGCAACTATGCCCAACGGTTGTTCCCGGGAATGCGGG
+TCAAATATGTCTCCACCGAGGAATTCACCAACGACTTCATTAACTCGCTCCGCGATGACCGCAAGGTCGC
+ATTCAAACGCAGCTACCGCGACGTAGACGTGCTGTTGGTCGACGACATCCAATTCATTGAAGGCAAAGAG
+GGTATTCAAGAGGAGTTCTTCCACACCTTCAACACCTTGCACAATGCCAACAAGCAAATCGTCATCTCAT
+CTGACCGCCCACCCAAGCAGCTCGCCACCCTCGAGGACCGGCTGAGAACCCGCTTTGAGTGGGGGCTGAT
+CACTGACGTACAACCACCCGAGCTGGAGACCCGCATCGCCATCTTGCGCAAGAAAGCACAGATGGAACGG
+CTCGCGATCCCCGACGATGTCCTCGAACTCATCGCCAGCAGTATCGAACGCAATATCCGTGAACTCGAGG
+GCGCGCTGATCCGGGTCACCGCGTTCGCCTCATTGAACAAAACACCAATCGACAAAGCGCTGGCCGAGAT
+TGTGCTTCGCGATCTGATCGCCGACGCCAACACCATGCAAATCAGCGCGGCGACGATCATGGCTGCCACC
+GCCGAATACTTCGACACTACCGTCGAAGAGCTTCGCGGGCCCGGCAAGACCCGAGCACTGGCCCAGTCAC
+GACAGATTGCGATGTACCTGTGTCGTGAGCTCACCGATCTTTCGTTGCCCAAAATCGGCCAAGCGTTCGG
+CCGTGATCACACAACCGTCATGTACGCCCAACGCAAGATCCTGTCCGAGATGGCCGAGCGCCGTGAGGTC
+TTTGATCACGTCAAAGAACTCACCACTCGCATCCGTCAGCGCTCCAAGCGCTAGCACGGCGTGTTCTTCC
+GACAACGTTCTTAAAAAAACTTCTCTCTCCCAGGTCACACCAGTCACAGAGATTGGCTGTGAGTGTCGCT
+GTGCACAAACCGCGCACAGACTCATACAGTCCCGGCGGTTCCGTTCACAACCCACGCCTCATCCCCACCG
+ACCCAACACACACCCCACAGTCATCGCCACCGTCATCCACAACTCCGACCGACGTCGACCTGCACCAAGA
+CCAGACTGTCCCCAAACTGCACACCCTCTAATACTGTTACCGAGATTTCTTCGTCGTTTGTTCTTGGAAA
+GACAGCGCTGGGGATCGTTCGCTGGATACCACCCGCATAACTGGCTCGTCGCGGTGGGTCAGAGGTCAAT
+GATGAACTTTCAAGTTGACGTGAGAAGCTCTACGGTTGTTGTTCGACTGCTGTTGCGGCCGTCGTGGCGG
+GTCACGCGTCATGGGCGTTCGTCGTTGGCAGTCCCCACGCTAGCGGGGCGCTAGCCACGGGATCGAACTC
+ATCGTGAGGTGAAAGGGCGCAATGGACGCGGCTACGACAAGAGTTGGCCTCACCGACTTGACGTTTCGTT
+TGCTACGAGAGTCTTTCGCCGATGCGGTGTCGTGGGTGGCTAAAAATCTGCCAGCCAGGCCCGCGGTGCC
+GGTGCTCTCCGGCGTGTTGTTGACCGGCTCGGACAACGGTCTGACGATTTCCGGATTCGACTACGAGGTT
+TCCGCCGAGGCCCAGGTTGGCGCTGAAATTGTTTCTCCTGGAAGCGTTTTAGTTTCTGGCCGATTGTTGT
+CCGATATTACCCGGGCGTTGCCTAACAAGCCCGTAGGCGTTCATGTCGAAGGTAACCGGGTCGCATTGAC
+CTGCGGTAACGCCAGGTTTTCGCTACCGACGATGCCAGTCGAGGATTATCCGACGCTGCCGACGCTGCCG
+GAAGAGACCGGATTGTTGCCTGCGGAATTATTCGCCGAGGCAATCAGTCAGGTCGCTATCGCCGCCGGCC
+GGGACGACACGCTGCCTATGTTGACCGGCATCCGGGTCGAAATCCTCGGTGAGACGGTGGTTTTGGCCGC
+TACCGACAGGTTTCGCCTGGCTGTTCGAGAACTGAAGTGGTCGGCGTCGTCGCCAGATATCGAAGCGGCT
+GTGCTGGTCCCGGCCAAGACGCTGGCCGAGGCCGCCAAAGCGGGCATCGGCGGCTCTGACGTTCGTTTGT
+CGTTGGGTACTGGGCCGGGGGTGGGCAAGGATGGCCTGCTCGGTATCAGTGGGAACGGCAAGCGCAGCAC
+CACGCGACTTCTTGATGCCGAGTTCCCGAAGTTTCGGCAGTTGCTACCAACCGAACACACCGCGGTGGCC
+ACCATGGACGTGGCCGAGTTGATCGAAGCGATCAAGCTGGTTGCGTTGGTAGCTGATCGGGGCGCGCAGG
+TGCGCATGGAGTTCGCTGATGGCAGCGTGCGGCTTTCTGCGGGTGCCGATGATGTTGGACGAGCCGAGGA
+AGATCTTGTTGTTGACTATGCCGGTGAACCATTGACGATTGCGTTTAACCCAACCTATCTAACGGACGGT
+TTGAGTTCGTTGCGCTCGGAGCGAGTGTCTTTCGGGTTTACGACTGCGGGTAAGCCTGCCTTGCTACGTC
+CGGTGTCCGGGGACGATCGCCCTGTGGCGGGTCTGAATGGCAACGGTCCGTTCCCGGCGGTGTCGACGGA
+CTATGTCTATCTGTTGATGCCGGTTCGGTTGCCGGGCTGAGCACTTGGCGCCCGGGTAGGTGTACGTCCG
+TCATTTGGGGCTGCGTGACTTCCGGTCCTGGGCATGTGTAGATCTGGAATTGCATCCAGGGCGGACGGTT
+TTTGTTGGGCCTAACGGTTATGGTAAGACGAATCTTATTGAGGCACTGTGGTATTCGACGACGTTAGGTT
+CGCACCGCGTTAGCGCCGATTTGCCGTTGATCCGGGTAGGTACCGATCGTGCGGTGATCTCCACGATCGT
+GGTGAACGACGGTAGAGAATGTGCCGTCGACCTCGAGATCGCCACGGGGCGAGTCAACAAAGCGCGATTG
+AATCGATCATCGGTCCGAAGTACACGTGATGTGGTCGGAGTGCTTCGAGCTGTGTTGTTTGCCCCTGAGG
+ATCTGGGGTTGGTTCGTGGGGATCCCGCTGACCGGCGGCGCTATCTGGATGATCTGGCGATCGTGCGTAG
+GCCTGCGATCGCTGCGGTACGAGCCGAATATGAGAGGGTGGTGCGCCAGCGGACGGCGTTATTGAAGTCC
+GTACCTGGAGCACGGTATCGGGGTGACCGGGGTGTGTTTGACACTCTTGAGGTATGGGACAGTCGTTTGG
+CGGAGCACGGGGCTGAACTGGTGGCCGCCCGCATCGATTTGGTCAACCAGTTGGCACCGGAAGTGAAGAA
+GGCATACCAGCTGTTGGCGCCGGAATCGCGATCGGCGTCTATCGGTTATCGGGCCAGCATGGATGTAACC
+GGTCCCAGCGAGCAGTCAGATACCGATCGGCAATTGTTAGCAGCTCGGCTGTTGGCGGCGCTGGCGGCCC
+GTCGGGATGCCGAACTCGAGCGTGGGGTTTGTCTAGTTGGTCCGCACCGTGACGACCTAATACTGCGACT
+AGGCGATCAACCCGCGAAAGGATTTGCTAGCCATGGGGAGGCGTGGTCGTTGGCGGTGGCACTGCGGTTG
+GCGGCCTATCAACTGTTACGCGTTGATGGTGGTGAGCCGGTGTTGTTGCTCGACGACGTGTTCGCCGAAC
+TGGATGTCATGCGCCGTCGAGCGTTGGCGACGGCGGCCGAGTCCGCCGAACAGGTGTTGGTGACTGCCGC
+GGTGCTCGAGGATATTCCCGCCGGCTGGGACGCCAGGCGGGTGCACATCGATGTGCGTGCCGATGACACC
+GGATCGATGTCGGTGGTTCTGCCATGACGGGTTCTGTTGACCGGCCCGACCAGAATCGCGGTGAGCGATT
+AATGAAGTCACCAGGGTTGGATTTGGTCAGGCGCACCCTGGACGAAGCTCGTGCTGCTGCCCGCGCGCGC
+GGACAAGACGCCGGTCGAGGGCGGGTCGCTTCCGTTGCGTCGGGTCGGGTGGCCGGACGGCGACGAAGCT
+GGTCGGGTCCGGGGCCCGACATTCGTGATCCACAACCGCTGGGTAAGGCCGCTCGTGAGCTGGCAAAGAA
+ACGCGGCTGGTCGGTGCGGGTCGCCGAGGGTATGGTGCTCGGCCAGTGGTCTGCGGTGGTCGGCCACCAG
+ATCGCCGAACATGCACGCCCGACTGCGCTAAACGACGGGGTGTTGAGCGTGATTGCGGAGTCGACGGCGT
+GGGCGACGCAGTTGAGGATCATGCAGGCCCAGCTTCTGGCCAAGATCGCCGCAGCGGTTGGCAACGATGT
+GGTGCGATCGCTAAAGATCACCGGGCCGGCGGCACCATCGTGGCGCAAGGGGCCTCGCCATATTGCCGGT
+AGGGGTCCGCGCGACACCTACGGATAACACGTCGATCGGCCCAGAACAAGGCGCTCCGGTCCCGGCCTGA
+GAGCCTCGAGGACGAAGCGGATCCGTATGCCGGACGTCGGGACGCACCAGGAAGAAAGATGTCCGACGCA
+CGGCGCGGTTAGATGGGTAAAAACGAGGCCAGAAGATCGGCCCTGGCGCCCGATCACGGTACAGTGGTGT
+GCGACCCCCTGCGGCGACTCAACCGCATGCACGCAACCCCTGAGGAGAGTATTCGGATCGTGGCTGCCCA
+GAAAAAGAAGGCCCAAGACGAATACGGCGCTGCGTCTATCACCATTCTCGAAGGGCTGGAGGCCGTCCGC
+AAACGTCCCGGCATGTACATTGGCTCGACCGGTGAGCGCGGTTTACACCATCTCATTTGGGAGGTGGTCG
+ACAACGCGGTCGACGAGGCGATGGCCGGTTATGCAACCACAGTGAACGTAGTGCTGCTTGAGGATGGCGG
+TGTCGAGGTCGCCGACGACGGCCGCGGCATTCCGGTCGCCACCCACGCCTCCGGCATACCGACCGTCGAC
+GTGGTGATGACACAACTACATGCCGGCGGCAAGTTCGACTCGGACGCGTATGCGATATCTGGTGGTCTGC
+ACGGCGTCGGCGTGTCGGTGGTTAACGCGCTATCCACCCGGCTCGAAGTCGAGATCAAGCGCGACGGGTA
+CGAGTGGTCTCAGGTTTATGAGAAGTCGGAACCCCTGGGCCTCAAGCAAGGGGCGCCGACCAAGAAGACG
+GGGTCAACGGTACGGTTCTGGGCCGACCCCGCTGTTTTCGAAACCACGGAATACGACTTCGAAACCGTCG
+CCCGCCGGCTGCAAGAGATGGCGTTCCTCAACAAGGGGCTGACCATCAACCTGACCGACGAGAGGGTGAC
+CCAAGACGAGGTCGTCGACGAAGTGGTCAGCGACGTCGCCGAGGCGCCGAAGTCGGCAAGTGAACGCGCA
+GCCGAATCCACTGCACCGCACAAAGTTAAGAGCCGCACCTTTCACTATCCGGGTGGCCTGGTGGACTTCG
+TGAAACACATCAACCGCACCAAGAACGCGATTCATAGCAGCATCGTGGACTTTTCCGGCAAGGGCACCGG
+GCACGAGGTGGAGATCGCGATGCAATGGAACGCCGGGTATTCGGAGTCGGTGCACACCTTCGCCAACACC
+ATCAACACCCACGAGGGCGGCACCCACGAAGAGGGCTTCCGCAGCGCGCTGACGTCGGTGGTGAACAAGT
+ACGCCAAGGACCGCAAGCTACTGAAGGACAAGGACCCCAACCTCACCGGTGACGATATCCGGGAAGGCCT
+GGCCGCTGTGATCTCGGTGAAGGTCAGCGAACCGCAGTTCGAGGGCCAGACCAAGACCAAGTTGGGCAAC
+ACCGAGGTCAAATCGTTTGTGCAGAAGGTCTGTAATGAACAGCTGACCCACTGGTTTGAAGCCAACCCCA
+CCGACTCGAAAGTCGTTGTGAACAAGGCTGTGTCCTCGGCGCAAGCCCGTATCGCGGCACGTAAGGCACG
+AGAGTTGGTGCGGCGTAAGAGCGCCACCGACATCGGTGGATTGCCCGGCAAGCTGGCCGATTGCCGTTCC
+ACGGATCCGCGCAAGTCCGAACTGTATGTCGTAGAAGGTGACTCGGCCGGCGGTTCTGCAAAAAGCGGTC
+GCGATTCGATGTTCCAGGCGATACTTCCGCTGCGCGGCAAGATCATCAATGTGGAGAAAGCGCGCATCGA
+CCGGGTGCTAAAGAACACCGAAGTTCAGGCGATCATCACGGCGCTGGGCACCGGGATCCACGACGAGTTC
+GATATCGGCAAGCTGCGCTACCACAAGATCGTGCTGATGGCCGACGCCGATGTTGACGGCCAACATATTT
+CCACGCTGTTGTTGACGTTGTTGTTCCGGTTCATGCGGCCGCTCATCGAGAACGGGCATGTGTTTTTGGC
+ACAACCGCCGCTGTACAAACTCAAGTGGCAGCGCAGTGACCCGGAATTCGCATACTCCGACCGCGAGCGC
b
diff -r 000000000000 -r 76bc4efa1aeb test-data/fasta_indexes.loc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fasta_indexes.loc Fri Jan 28 12:21:05 2022 +0000
b
@@ -0,0 +1,1 @@
+89 89 Mycobacterium_AF2122 ${__HERE__}/NC_002945v4.fasta
b
diff -r 000000000000 -r 76bc4efa1aeb test-data/input0.fasta.gz
b
Binary file test-data/input0.fasta.gz has changed
b
diff -r 000000000000 -r 76bc4efa1aeb test-data/input1.bam
b
Binary file test-data/input1.bam has changed
b
diff -r 000000000000 -r 76bc4efa1aeb test-data/input2.bam
b
Binary file test-data/input2.bam has changed
b
diff -r 000000000000 -r 76bc4efa1aeb test-data/input_depth1.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input_depth1.tabular Fri Jan 28 12:21:05 2022 +0000
b
@@ -0,0 +1,2 @@
+contigName contigLen totalAvgDepth dataset_2272.dat dataset_2272.dat-var
+NC_002945.4 Mycobacterium bovis AF2122/97 genome assembly, chromosome: Mycobacterium_bovis_AF2122/97 7000 0 0 0
b
diff -r 000000000000 -r 76bc4efa1aeb test-data/jgi_output1.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/jgi_output1.tabular Fri Jan 28 12:21:05 2022 +0000
b
@@ -0,0 +1,2 @@
+contigName contigLen totalAvgDepth
+gi|251831106|ref|NC_012920.1| 16569 0.667885 0.667885 50.6321
b
diff -r 000000000000 -r 76bc4efa1aeb test-data/jgi_output2.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/jgi_output2.tabular Fri Jan 28 12:21:05 2022 +0000
b
@@ -0,0 +1,2 @@
+contigName contigLen totalAvgDepth
+gi|251831106|ref|NC_012920.1| 16569 1.33577 0.667885 50.6321 0.667885 50.6321
b
diff -r 000000000000 -r 76bc4efa1aeb test-data/jgi_output_depth1.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/jgi_output_depth1.tabular Fri Jan 28 12:21:05 2022 +0000
b
@@ -0,0 +1,2 @@
+contigName contigLen totalAvgDepth
+NC_002945.4 Mycobacterium bovis AF2122/97 genome assembly, chromosome: Mycobacterium_bovis_AF2122/97 7000 0 0 0
b
diff -r 000000000000 -r 76bc4efa1aeb test-data/jgi_output_gc1.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/jgi_output_gc1.tabular Fri Jan 28 12:21:05 2022 +0000
b
@@ -0,0 +1,102 @@
+GC Ref Reads Coverage Mean Variance
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b
diff -r 000000000000 -r 76bc4efa1aeb test-data/jgi_output_kmers1.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/jgi_output_kmers1.tabular Fri Jan 28 12:21:05 2022 +0000
b
@@ -0,0 +1,257 @@
+Kmer MappedReadCount UnmappedReadCount MappedKmers NumMappedReads Mean Variance Skewness Kurtosis
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b
diff -r 000000000000 -r 76bc4efa1aeb test-data/jgi_output_read_stats1.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/jgi_output_read_stats1.tabular Fri Jan 28 12:21:05 2022 +0000
b
@@ -0,0 +1,1 @@
+ReadName ReadLen AlignedLen PctId MappedTID MappedPos ExactMatches Substitutions Insertions Deletions SoftClips HardClips PctId2 PctId3 PctId4 PctId5 PctId6 PctId7 PctId8 NM ReadGC MappedGC
b
diff -r 000000000000 -r 76bc4efa1aeb test-data/process_log.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/process_log.txt Fri Jan 28 12:21:05 2022 +0000
b
@@ -0,0 +1,3 @@
+MetaBAT 2 (2.15 (Bioconda)) using minContig 1500, minCV 1.0, minCVSum 1.0, maxP 95%, minS 60, maxEdges 200 and minClsSize 200000. with random seed=345678
+No edges were formed by TNF.
+0 bins (0 bases in total) formed.
b
diff -r 000000000000 -r 76bc4efa1aeb tool-data/fasta_indexes.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/fasta_indexes.loc.sample Fri Jan 28 12:21:05 2022 +0000
b
@@ -0,0 +1,29 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of Samtools indexed sequences data files.  You will need
+#to create these data files and then create a fasta_indexes.loc file
+#similar to this one (store it in this directory) that points to
+#the directories in which those files are stored. The fasta_indexes.loc
+#file has this format (white space characters are TAB characters):
+#
+# <unique_build_id> <dbkey> <display_name> <file_base_path>
+#
+#So, for example, if you had hg19 Canonical indexed stored in
+#
+# /depot/data2/galaxy/hg19/sam/,
+#
+#then the fasta_indexes.loc entry would look like this:
+#
+#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa
+#
+#and your /depot/data2/galaxy/hg19/sam/ directory
+#would contain hg19canon.fa and hg19canon.fa.fai files.
+#
+#Your fasta_indexes.loc file should include an entry per line for
+#each index set you have stored.  The file in the path does actually
+#exist, but it should never be directly used. Instead, the name serves
+#as a prefix for the index file.  For example:
+#
+#hg18canon hg18 Human (Homo sapiens): hg18 Canonical /depot/data2/galaxy/hg18/sam/hg18canon.fa
+#hg18full hg18 Human (Homo sapiens): hg18 Full /depot/data2/galaxy/hg18/sam/hg18full.fa
+#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa
+#hg19full hg19 Human (Homo sapiens): hg19 Full /depot/data2/galaxy/hg19/sam/hg19full.fa
b
diff -r 000000000000 -r 76bc4efa1aeb tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Fri Jan 28 12:21:05 2022 +0000
b
@@ -0,0 +1,8 @@
+<tables>
+    <!-- Location of SAMTools indexes for FASTA files -->
+    <table name="fasta_indexes" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/fasta_indexes.loc" />
+    </table>
+</tables>
+
b
diff -r 000000000000 -r 76bc4efa1aeb tool_data_table_conf.xml.test
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test Fri Jan 28 12:21:05 2022 +0000
b
@@ -0,0 +1,7 @@
+<tables>
+    <table name="fasta_indexes" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="${__HERE__}/test-data/fasta_indexes.loc" />
+    </table>
+</tables>
+