# HG changeset patch
# User iuc
# Date 1465334760 14400
# Node ID 501c21cce6149a7bacdd4f7ce75c9e9adc2cd36b

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e

diff -r 000000000000 -r 501c21cce614 biom_convert.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/biom_convert.xml	Tue Jun 07 17:26:00 2016 -0400
@@ -0,0 +1,182 @@
+<tool id="biom_convert" name="Convert BIOM" version="@VERSION@.0">
+    <description>formats</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <expand macro="version_command" />
+    <command>
+        <![CDATA[
+            biom convert -i "${input_type.input_table}" -o "${output_table}"
+            #if str( $input_type.input_type_selector ) == "tsv": 
+                #if $input_type.process_obs_metadata:
+                    --process-obs-metadata "${input_type.process_obs_metadata}"
+                #end if
+            #end if
+
+            #if str( $output_type.output_type_selector ) == "tsv": 
+                --to-tsv
+                #if $output_type.header_key:
+                    --header-key "${output_type.header_key}"
+                    #if $output_type.output_metadata_id:
+                        --output-metadata-id "${output_type.output_metadata_id}"
+                    #end if
+                    --tsv-metadata-formatter "${output_type.tsv_metadata_formatter}"
+                #end if
+            #else:
+                --table-type "${output_type.table_type}"
+                #if str( $output_type.biom_type.biom_type_selector ) == 'hdf5':
+                    --to-hdf5
+                    ${output_type.biom_type.collapsed_samples}
+                    ${output_type.biom_type.collapsed_observations}
+                #else:
+                    --to-json
+                #end if
+                #if $output_type.sample_metadata_fp:
+                    --sample-metadata-fp "${output_type.sample_metadata_fp}"
+                #end if
+                #if $output_type.observation_metadata_fp:
+                    --observation-metadata-fp "${output_type.observation_metadata_fp}"
+                #end if
+            #end if   
+        ]]>
+    </command>
+    <inputs>
+        <conditional name="input_type">
+            <param name="input_type_selector" type="select" label="Choose the source BIOM format">
+                <option value="tsv" selected="True">Tabular File</option>
+                <option value="biom">BIOM File</option>
+            </param>
+            <when value="tsv">
+                <param name="input_table" type="data" format="tabular" label="Tabular File" argument="--input-fp"/>
+                <param name="process_obs_metadata" type="select" label="Process metadata associated with observations when converting" argument="--process-obs-metadata">
+                    <option value="" selected="True">Do Not process metadata</option>
+                    <option value="taxonomy">taxonomy</option>
+                    <option value="naive">naive</option>
+                    <option value="sc_separated">sc_separated</option>
+                </param>
+            </when>
+            <when value="biom">
+                <param name="input_table" type="data" format="biom1" label="Tabular File" argument="--input-fp"/>
+            </when>
+        </conditional>
+        <conditional name="output_type">
+            <param name="output_type_selector" type="select" label="Choose the output type" argument="--to-tsv">
+                <option value="tsv">TSV-formatted (classic) table</option>
+                <option value="biom" selected="True">BIOM</option>
+            </param>
+            <when value="tsv">
+                <param name="header_key" type="text" value="" label="observation metadata to include" help="Leave empty to ignore" argument="--header-key"/>
+                <param name="output_metadata_id" type="text" value="" label="name to be given to the observation metadata column" help="Leave empty to ignore" argument="--output-metadata-id"/>
+                <param name="tsv_metadata_formatter" type="select" label="Method for formatting the observation metadata" argumet="--tsv-metadata-formatter">
+                    <option value="naive" selected="True">naive</option>
+                    <option value="sc_separated">Semi-colon separated</option>
+                </param>
+            </when>
+            <when value="biom">
+                <param name="table_type" type="select" label="Table Type" argument="--table-type">
+                    <option value="OTU table">OTU table</option>
+                    <option value="Pathway table">Pathway table</option>
+                    <option value="Function table">Function table</option>
+                    <option value="Ortholog table">Ortholog table</option>
+                    <option value="Gene table">Gene table</option>
+                    <option value="Metabolite table">Metabolite table</option>
+                    <option value="Taxon table">Taxon table</option>
+                    <option value="Table" selected="True">Table</option>
+                </param>
+                <conditional name="biom_type">
+                    <param name="biom_type_selector" type="select" label="BIOM format type" argument="--to-json / --to-hdf5">
+                        <option value="json" selected="True">JSON-formatted table (BIOM1)</option>
+                        <option value="hdf5">HDF5-formatted table (BIOM2)</option>
+                    </param>
+                    <when value="json">
+                    </when>
+                    <when value="hdf5">
+                        <param name="collapsed_samples" type="boolean" truevalue="" falsevalue="--collapsed-samples" checked="False" label="Use collapsed samples" argument="--collapsed-observations"/>
+                        <param name="collapsed_observations" type="boolean" truevalue="" falsevalue="--collapsed-samples" checked="False" label="Use collapsed observations"/>
+                    </when>
+                </conditional>
+                <param name="sample_metadata_fp" type="data" format="tabular" optional="True" label="Add sample metadata from metadata mapping file" argument="--sample-metadata-fp"/>
+                <param name="observation_metadata_fp" type="data" format="tabular" optional="True" label="Add observation metadata from mapping file" argument="--observation-metadata-fp"/>
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data format="biom1" name="output_table">
+            <change_format>
+                <when input="output_type.output_type_selector" value="tsv" format="tabular" />
+                <when input="output_type.biom_type" value="hdf5" format="biom2" />
+            </change_format>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <conditional name="input_type">
+                <param name="input_type_selector" value="tsv"/>
+                <param name="input_table" value="input_abundance_taxonomy_1.tabular" ftype="tabular"/>
+                <param name="process_obs_metadata" value="taxonomy"/>
+            </conditional>
+            <conditional name="output_type">
+                <param name="output_type_selector" value="biom"/>
+                <param name="table_type" value="OTU table"/>
+                <conditional name="biom_type">
+                    <param name="biom_type_selector" value="json"/>
+                </conditional>
+                <param name="sample_metadata_fp"/>
+                <param name="observation_metadata_fp"/>
+            </conditional>
+            <output name="output_table" file="output_taxonomy_1.biom1.re" ftype="biom1" compare="re_match"/>
+        </test>
+        <test>
+            <conditional name="input_type">
+                <param name="input_type_selector" value="tsv"/>
+                <param name="input_table" value="input_abundance_1.tabular" ftype="tabular"/>
+                <param name="process_obs_metadata" value=""/>
+            </conditional>
+            <conditional name="output_type">
+                <param name="output_type_selector" value="biom"/>
+                <param name="table_type" value="OTU table"/>
+                <conditional name="biom_type">
+                    <param name="biom_type_selector" value="json"/>
+                </conditional>
+                <param name="sample_metadata_fp"/>
+                <param name="observation_metadata_fp"/>
+            </conditional>
+            <output name="output_table" file="output_1.biom1.re" ftype="biom1" compare="re_match"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+Usage: biom convert [OPTIONS]::
+
+  Convert to/from the BIOM table format.
+
+  Convert between BIOM table formats. See examples here: http://biom-format.org/documentation/biom_conversion.html
+
+  Example usage:
+
+  Convert a "classic" BIOM file (tab-separated text) to an HDF5 BIOM formatted OTU table:
+
+  $ biom convert -i table.txt -o table.biom --to-hdf5
+
+
+Options:
+  -i, --input-fp PATH             The input BIOM table  [required]
+  -o, --output-fp PATH            The output BIOM table  [required]
+  -m, --sample-metadata-fp PATH   The sample metadata mapping file (will add sample metadata to the input BIOM table, if provided).
+  --observation-metadata-fp PATH  The observation metadata mapping file (will add observation metadata to the input BIOM table, if provided).
+  --to-json                       Output as JSON-formatted table.
+  --to-hdf5                       Output as HDF5-formatted table.
+  --to-tsv                        Output as TSV-formatted (classic) table. table is a BIOM table with collapsed samples, this will update the sample metadata of the table to the supported HDF5 collapsed format.
+  --collapsed-observations        If --to_hdf5 is passed and the original table is a BIOM table with collapsed observations, this will update the  supported HDF5 collapsed format.
+  --header-key TEXT               The observation metadata to include from the input BIOM table file when creating a tsv table file. By default no observation metadata will be included.
+  --output-metadata-id TEXT       The name to be given to the observation metadata column when creating a tsv table file if the column should be renamed.
+  --table-type                    OTU table,Pathway table,Function table,Ortholog table,Gene table,Metabolite table,Taxon table,Table The type of the table.
+  --process-obs-metadata          taxonomy,naive,sc_separated Process metadata associated with observations when converting from a classic table.
+  --tsv-metadata-formatter        naive,sc_separated Method for formatting the observation 
+  --help                          Show this message and exit.
+
+    ]]></help>
+    <expand macro="citations" />
+</tool>
diff -r 000000000000 -r 501c21cce614 macros.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Tue Jun 07 17:26:00 2016 -0400
@@ -0,0 +1,24 @@
+<macros>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="2.1.5">biom-format</requirement>
+            <yield/>
+        </requirements>
+    </xml>
+    <token name="@VERSION@">2.1.5</token>
+    <xml name="stdio">
+        <stdio>
+            <exit_code range="1:" />
+            <exit_code range=":-1" />
+        </stdio>
+    </xml>
+    <xml name="version_command">
+        <version_command>biom --version</version_command>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1186/2047-217X-1-7</citation>
+            <yield/>
+        </citations>
+    </xml>
+</macros>
diff -r 000000000000 -r 501c21cce614 test-data/input_abundance_1.biom1
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input_abundance_1.biom1	Tue Jun 07 17:26:00 2016 -0400
@@ -0,0 +1,1 @@
+{"id": "None","format": "Biological Observation Matrix 1.0.0","format_url": "http://biom-format.org","matrix_type": "sparse","generated_by": "BIOM-Format 2.1.5","date": "2016-05-26T17:20:40.263567","type": "OTU table","matrix_element_type": "float","shape": [19, 2],"data": [[1,0,160.0],[1,1,242.0],[6,0,1.0],[6,1,1.0],[7,0,3.0],[7,1,4.0],[12,0,13.0],[12,1,36.0],[14,0,1.0],[14,1,5.0],[15,0,1.0],[16,0,1.0],[16,1,3.0]],"rows": [{"id": "2", "metadata": null},{"id": "3", "metadata": null},{"id": "4", "metadata": null},{"id": "5", "metadata": null},{"id": "8", "metadata": null},{"id": "9", "metadata": null},{"id": "10", "metadata": null},{"id": "11", "metadata": null},{"id": "12", "metadata": null},{"id": "14", "metadata": null},{"id": "15", "metadata": null},{"id": "16", "metadata": null},{"id": "17", "metadata": null},{"id": "18", "metadata": null},{"id": "22", "metadata": null},{"id": "23", "metadata": null},{"id": "25", "metadata": null},{"id": "28", "metadata": null},{"id": "29", "metadata": null}],"columns": [{"id": "SAMPLE_1", "metadata": null},{"id": "SAMPLE_2", "metadata": null}]}
\ No newline at end of file
diff -r 000000000000 -r 501c21cce614 test-data/input_abundance_1.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input_abundance_1.tabular	Tue Jun 07 17:26:00 2016 -0400
@@ -0,0 +1,20 @@
+#ID	SAMPLE_1	SAMPLE_2
+2	0	0
+3	160	242
+4	0	0
+5	0	0
+8	0	0
+9	0	0
+10	1	1
+11	3	4
+12	0	0
+14	0	0
+15	0	0
+16	0	0
+17	13	36
+18	0	0
+22	1	5
+23	1	0
+25	1	3
+28	0	0
+29	0	0
diff -r 000000000000 -r 501c21cce614 test-data/input_abundance_taxonomy_1.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input_abundance_taxonomy_1.tabular	Tue Jun 07 17:26:00 2016 -0400
@@ -0,0 +1,20 @@
+#ID	SAMPLE_1	SAMPLE_2	taxonomy
+2	0	0	d__Archaea
+3	160	242	d__Bacteria
+4	0	0	d__Archaea;p__Crenarchaeota
+5	0	0	d__Archaea;p__Euryarchaeota
+8	0	0	d__Bacteria;p__AC1
+9	0	0	d__Bacteria;p__AD3
+10	1	1	d__Bacteria;p__Acidobacteria
+11	3	4	d__Bacteria;p__Actinobacteria
+12	0	0	d__Bacteria;p__AncK6
+14	0	0	d__Bacteria;p__Armatimonadetes
+15	0	0	d__Bacteria;p__BHI80-139
+16	0	0	d__Bacteria;p__BRC1
+17	13	36	d__Bacteria;p__Bacteroidetes
+18	0	0	d__Bacteria;p__CD12
+22	1	5	d__Bacteria;p__Chlorobi
+23	1	0	d__Bacteria;p__Chloroflexi
+25	1	3	d__Bacteria;p__Cyanobacteria
+28	0	0	d__Bacteria;p__EM19
+29	0	0	d__Bacteria;p__EM3
diff -r 000000000000 -r 501c21cce614 test-data/input_taxonomy_1.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input_taxonomy_1.tabular	Tue Jun 07 17:26:00 2016 -0400
@@ -0,0 +1,20 @@
+#ID	taxonomy
+2	d__Archaea
+3	d__Bacteria
+4	d__Archaea;p__Crenarchaeota
+5	d__Archaea;p__Euryarchaeota
+8	d__Bacteria;p__AC1
+9	d__Bacteria;p__AD3
+10	d__Bacteria;p__Acidobacteria
+11	d__Bacteria;p__Actinobacteria
+12	d__Bacteria;p__AncK6
+14	d__Bacteria;p__Armatimonadetes
+15	d__Bacteria;p__BHI80-139
+16	d__Bacteria;p__BRC1
+17	d__Bacteria;p__Bacteroidetes
+18	d__Bacteria;p__CD12
+22	d__Bacteria;p__Chlorobi
+23	d__Bacteria;p__Chloroflexi
+25	d__Bacteria;p__Cyanobacteria
+28	d__Bacteria;p__EM19
+29	d__Bacteria;p__EM3
diff -r 000000000000 -r 501c21cce614 test-data/output_1.biom1.re
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output_1.biom1.re	Tue Jun 07 17:26:00 2016 -0400
@@ -0,0 +1,1 @@
+\{\"id\"\:\ \"None\"\,\"format\"\:\ \"Biological\ Observation\ Matrix\ 1\.0\.0\"\,\"format\_url\"\:\ \"http\:\/\/biom\-format\.org\"\,\"matrix\_type\"\:\ \"sparse\"\,\"generated\_by\"\:\ \"BIOM\-Format\ 2\.1\.5\"\,\"date\"\:\ \".*\"\,\"type\"\:\ \"OTU\ table\"\,\"matrix\_element\_type\"\:\ \"float\"\,\"shape\"\:\ \[19\,\ 2\]\,\"data\"\:\ \[\[1\,0\,160\.0\]\,\[1\,1\,242\.0\]\,\[6\,0\,1\.0\]\,\[6\,1\,1\.0\]\,\[7\,0\,3\.0\]\,\[7\,1\,4\.0\]\,\[12\,0\,13\.0\]\,\[12\,1\,36\.0\]\,\[14\,0\,1\.0\]\,\[14\,1\,5\.0\]\,\[15\,0\,1\.0\]\,\[16\,0\,1\.0\]\,\[16\,1\,3\.0\]\]\,\"rows\"\:\ \[\{\"id\"\:\ \"2\"\,\ \"metadata\"\:\ null\}\,\{\"id\"\:\ \"3\"\,\ \"metadata\"\:\ null\}\,\{\"id\"\:\ \"4\"\,\ \"metadata\"\:\ null\}\,\{\"id\"\:\ \"5\"\,\ \"metadata\"\:\ null\}\,\{\"id\"\:\ \"8\"\,\ \"metadata\"\:\ null\}\,\{\"id\"\:\ \"9\"\,\ \"metadata\"\:\ null\}\,\{\"id\"\:\ \"10\"\,\ \"metadata\"\:\ null\}\,\{\"id\"\:\ \"11\"\,\ \"metadata\"\:\ null\}\,\{\"id\"\:\ \"12\"\,\ \"metadata\"\:\ null\}\,\{\"id\"\:\ \"14\"\,\ \"metadata\"\:\ null\}\,\{\"id\"\:\ \"15\"\,\ \"metadata\"\:\ null\}\,\{\"id\"\:\ \"16\"\,\ \"metadata\"\:\ null\}\,\{\"id\"\:\ \"17\"\,\ \"metadata\"\:\ null\}\,\{\"id\"\:\ \"18\"\,\ \"metadata\"\:\ null\}\,\{\"id\"\:\ \"22\"\,\ \"metadata\"\:\ null\}\,\{\"id\"\:\ \"23\"\,\ \"metadata\"\:\ null\}\,\{\"id\"\:\ \"25\"\,\ \"metadata\"\:\ null\}\,\{\"id\"\:\ \"28\"\,\ \"metadata\"\:\ null\}\,\{\"id\"\:\ \"29\"\,\ \"metadata\"\:\ null\}\]\,\"columns\"\:\ \[\{\"id\"\:\ \"SAMPLE\_1\"\,\ \"metadata\"\:\ null\}\,\{\"id\"\:\ \"SAMPLE\_2\"\,\ \"metadata\"\:\ null\}\]\}
diff -r 000000000000 -r 501c21cce614 test-data/output_taxonomy_1.biom1.re
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output_taxonomy_1.biom1.re	Tue Jun 07 17:26:00 2016 -0400
@@ -0,0 +1,1 @@
+\{\"id\"\:\ \"None\"\,\"format\"\:\ \"Biological\ Observation\ Matrix\ 1\.0\.0\"\,\"format\_url\"\:\ \"http\:\/\/biom\-format\.org\"\,\"matrix\_type\"\:\ \"sparse\"\,\"generated\_by\"\:\ \"BIOM\-Format\ 2\.1\.5\"\,\"date\"\:\ \".*\"\,\"type\"\:\ \"OTU\ table\"\,\"matrix\_element\_type\"\:\ \"float\"\,\"shape\"\:\ \[19\,\ 2\]\,\"data\"\:\ \[\[1\,0\,160\.0\]\,\[1\,1\,242\.0\]\,\[6\,0\,1\.0\]\,\[6\,1\,1\.0\]\,\[7\,0\,3\.0\]\,\[7\,1\,4\.0\]\,\[12\,0\,13\.0\]\,\[12\,1\,36\.0\]\,\[14\,0\,1\.0\]\,\[14\,1\,5\.0\]\,\[15\,0\,1\.0\]\,\[16\,0\,1\.0\]\,\[16\,1\,3\.0\]\]\,\"rows\"\:\ \[\{\"id\"\:\ \"2\"\,\ \"metadata\"\:\ \{\"taxonomy\"\:\ \[\"d\_\_Archaea\"\]\}\}\,\{\"id\"\:\ \"3\"\,\ \"metadata\"\:\ \{\"taxonomy\"\:\ \[\"d\_\_Bacteria\"\]\}\}\,\{\"id\"\:\ \"4\"\,\ \"metadata\"\:\ \{\"taxonomy\"\:\ \[\"d\_\_Archaea\"\,\ \"p\_\_Crenarchaeota\"\]\}\}\,\{\"id\"\:\ \"5\"\,\ \"metadata\"\:\ \{\"taxonomy\"\:\ \[\"d\_\_Archaea\"\,\ \"p\_\_Euryarchaeota\"\]\}\}\,\{\"id\"\:\ \"8\"\,\ \"metadata\"\:\ \{\"taxonomy\"\:\ \[\"d\_\_Bacteria\"\,\ \"p\_\_AC1\"\]\}\}\,\{\"id\"\:\ \"9\"\,\ \"metadata\"\:\ \{\"taxonomy\"\:\ \[\"d\_\_Bacteria\"\,\ \"p\_\_AD3\"\]\}\}\,\{\"id\"\:\ \"10\"\,\ \"metadata\"\:\ \{\"taxonomy\"\:\ \[\"d\_\_Bacteria\"\,\ \"p\_\_Acidobacteria\"\]\}\}\,\{\"id\"\:\ \"11\"\,\ \"metadata\"\:\ \{\"taxonomy\"\:\ \[\"d\_\_Bacteria\"\,\ \"p\_\_Actinobacteria\"\]\}\}\,\{\"id\"\:\ \"12\"\,\ \"metadata\"\:\ \{\"taxonomy\"\:\ \[\"d\_\_Bacteria\"\,\ \"p\_\_AncK6\"\]\}\}\,\{\"id\"\:\ \"14\"\,\ \"metadata\"\:\ \{\"taxonomy\"\:\ \[\"d\_\_Bacteria\"\,\ \"p\_\_Armatimonadetes\"\]\}\}\,\{\"id\"\:\ \"15\"\,\ \"metadata\"\:\ \{\"taxonomy\"\:\ \[\"d\_\_Bacteria\"\,\ \"p\_\_BHI80\-139\"\]\}\}\,\{\"id\"\:\ \"16\"\,\ \"metadata\"\:\ \{\"taxonomy\"\:\ \[\"d\_\_Bacteria\"\,\ \"p\_\_BRC1\"\]\}\}\,\{\"id\"\:\ \"17\"\,\ \"metadata\"\:\ \{\"taxonomy\"\:\ \[\"d\_\_Bacteria\"\,\ \"p\_\_Bacteroidetes\"\]\}\}\,\{\"id\"\:\ \"18\"\,\ \"metadata\"\:\ \{\"taxonomy\"\:\ \[\"d\_\_Bacteria\"\,\ \"p\_\_CD12\"\]\}\}\,\{\"id\"\:\ \"22\"\,\ \"metadata\"\:\ \{\"taxonomy\"\:\ \[\"d\_\_Bacteria\"\,\ \"p\_\_Chlorobi\"\]\}\}\,\{\"id\"\:\ \"23\"\,\ \"metadata\"\:\ \{\"taxonomy\"\:\ \[\"d\_\_Bacteria\"\,\ \"p\_\_Chloroflexi\"\]\}\}\,\{\"id\"\:\ \"25\"\,\ \"metadata\"\:\ \{\"taxonomy\"\:\ \[\"d\_\_Bacteria\"\,\ \"p\_\_Cyanobacteria\"\]\}\}\,\{\"id\"\:\ \"28\"\,\ \"metadata\"\:\ \{\"taxonomy\"\:\ \[\"d\_\_Bacteria\"\,\ \"p\_\_EM19\"\]\}\}\,\{\"id\"\:\ \"29\"\,\ \"metadata\"\:\ \{\"taxonomy\"\:\ \[\"d\_\_Bacteria\"\,\ \"p\_\_EM3\"\]\}\}\]\,\"columns\"\:\ \[\{\"id\"\:\ \"SAMPLE\_1\"\,\ \"metadata\"\:\ null\}\,\{\"id\"\:\ \"SAMPLE\_2\"\,\ \"metadata\"\:\ null\}\]\}