Repository 'humann2_split_table'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/humann2_split_table

Changeset 1:ace84aac38ce (2017-08-01)
Previous changeset 0:8ed686bd4229 (2017-03-13) Next changeset 2:b35c9aea01ed (2017-11-09)
Commit message:
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
modified:
generate_test_data
humann2_macros.xml
humann2_split_table.xml
repository_dependencies.xml
added:
static/images/731303924-page_DENITRIFICATION-PWY.png
test-data/barplot1.png
test-data/barplot2.pdf
test-data/barplot3.svg
test-data/barplot4.png
test-data/hmp_pathabund.txt
test-data/rename_mapping
test-data/rna_dna_norm-dna.txt
test-data/rna_dna_norm-rna.txt
test-data/strain_profiler-input.txt
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diff -r 8ed686bd4229 -r ace84aac38ce generate_test_data
--- a/generate_test_data Mon Mar 13 12:37:33 2017 -0400
+++ b/generate_test_data Tue Aug 01 07:57:15 2017 -0400
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@@ -48,6 +48,66 @@
     --output-basename 'humann2' \
     --pathways 'unipathway'
 
+# humann2_associate
+humann2_associate \
+    --input 'test-data/hmp_pathabund.txt' \
+    --focal-metadatum 'STSite' \
+    --last-metadatum 'STSite' \
+    --focal-type 'categorical' \
+    --fdr '0.2' \
+    --output 'test-data/associate_output.txt'
+
+# humann2_barplot
+humann2_barplot \
+    --input 'test-data/hmp_pathabund.txt' \
+    --focal-feature ANAGLYCOLYSIS-PWY \
+    --sort none \
+    --last-metadatum STSite \
+    --focal-metadatum STSite \
+    --scaling none \
+    --width 5 \
+    --dimensions 8 4 \
+    --output test-data/barplot1.png
+
+humann2_barplot \
+    --input 'test-data/hmp_pathabund.txt' \
+    --focal-feature ANAGLYCOLYSIS-PWY \
+    --sort sum \
+    --last-metadatum STSite \
+    --focal-metadatum STSite \
+    --scaling pseudolog \
+    --width 5 \
+    --dimensions 8 4 \
+    --output test-data/barplot2.pdf
+
+humann2_barplot \
+    --input 'test-data/hmp_pathabund.txt' \
+    --focal-feature ANAGLYCOLYSIS-PWY \
+    --sort metadata \
+    --last-metadatum STSite \
+    --focal-metadatum STSite \
+    --exclude-unclassified \
+    --scaling none \
+    --as-genera \
+    --grid \
+    --remove-zeroes \
+    --width 5 \
+    --dimensions 8 4 \
+    --output test-data/barplot3.svg
+
+humann2_barplot \
+    --input 'test-data/hmp_pathabund.txt' \
+    --focal-feature ANAGLYCOLYSIS-PWY \
+    --top-strata 12 \
+    --sort sum \
+    --last-metadatum STSite \
+    --focal-metadatum STSite \
+    --exclude-unclassified \
+    --scaling normalize \
+    --width 5 \
+    --dimensions 8 4 \
+    --output test-data/barplot4.eps
+
 # humann2_regroup_table
 humann2_regroup_table \
     --input 'test-data/demo_genefamilies.tsv' \
@@ -111,9 +171,34 @@
 
 # humann2_rename_table
 humann2_rename_table \
+    --input 'test-data/regrouped_gene_families_to_infogo1000.tsv' \
+    --names 'infogo1000' \
+    -o 'test-data/renamed_info1000.tsv'
+    
+humann2_rename_table \
+    --input 'test-data/regrouped_gene_families_to_infogo1000.tsv' \
+    --custom 'test-data/rename_mapping' \
+    -o 'test-data/renamed_mapping_info1000.tsv'
+
+# humann2_rna_dna_norm
+humann2_rna_dna_norm \
+    --input_dna 'test-data/rna_dna_norm-dna.txt' \
+    --input_rna 'test-data/rna_dna_norm-rna.txt' \
+    --output_basename 'results1' \
+    --method 'laplace'
+
+humann2_rna_dna_norm \
+    --input_dna 'test-data/rna_dna_norm-dna.txt' \
+    --input_rna 'test-data/rna_dna_norm-rna.txt' \
+    --output_basename 'results2' \
+    --method 'witten_bell' \
+    --log_transform \
+    --log_base '2'
+
+# humann2_split_stratified_table
+humann2_split_stratified_table \
     --input 'test-data/demo_genefamilies.tsv' \
-    -o 'test-data/renamed_genefamilies.tsv' \
-    --names 'metacyc-pwy'
+    --output 'split_stratified_table'
 
 # humann2_split_table
 mkdir split_table_tmp_dir
@@ -122,3 +207,23 @@
     -o 'split_table_tmp_dir'
 cp 'split_table_tmp_dir/demo_Abundance.tsv' 'test-data/'
 cp 'split_table_tmp_dir/demo_Coverage.tsv' 'test-data/'
+
+# humann2_strain_profiler
+humann2_strain_profiler \
+    --input 'test-data/strain_profiler-input.txt' \
+    --critical_mean '1' \
+    --critical_count '2' \
+    --pinterval '1e-10' '1' \
+    --critical_samples '2'
+
+# humann2_unpack_pathways
+humann2_unpack_pathways \
+    --input-genes 'test-data/demo_genefamilies.tsv' \
+    --input-pathways 'test-data/demo_pathabundance.tsv' \
+    --output unpack1
+
+humann2_unpack_pathways \
+    --input-genes 'test-data/demo_genefamilies.tsv' \
+    --input-pathways 'test-data/demo_pathabundance.tsv' \
+    --remove-taxonomy \
+    --output unpack2
b
diff -r 8ed686bd4229 -r ace84aac38ce humann2_macros.xml
--- a/humann2_macros.xml Mon Mar 13 12:37:33 2017 -0400
+++ b/humann2_macros.xml Tue Aug 01 07:57:15 2017 -0400
b
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <macros>
-    <token name="@WRAPPER_VERSION@">0.9.9</token>
+    <token name="@WRAPPER_VERSION@">0.11.1</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@WRAPPER_VERSION@">humann2</requirement>
b
diff -r 8ed686bd4229 -r ace84aac38ce humann2_split_table.xml
--- a/humann2_split_table.xml Mon Mar 13 12:37:33 2017 -0400
+++ b/humann2_split_table.xml Tue Aug 01 07:57:15 2017 -0400
[
@@ -6,15 +6,15 @@
     <expand macro="requirements"/>
     <expand macro="version"/>
     <command detect_errors="exit_code"><![CDATA[
-        humann2_split_table
-            --input '$input'
-            -o 'output'
-            #if $taxonomy_index
-                --taxonomy_index '$taxonomy_index'
-            #end if
-            #if $taxonomy_level
-                --taxonomy_level '$taxonomy_level'
-            #end if
+humann2_split_table
+    --input '$input'
+    -o 'output'
+    #if $taxonomy_index
+        --taxonomy_index '$taxonomy_index'
+    #end if
+    #if $taxonomy_level
+        --taxonomy_level '$taxonomy_level'
+    #end if
     ]]></command>
     <inputs>
         <param argument="--input" type="data" format="tsv,tabular,biom1" label="Gene table to split"/>
b
diff -r 8ed686bd4229 -r ace84aac38ce repository_dependencies.xml
--- a/repository_dependencies.xml Mon Mar 13 12:37:33 2017 -0400
+++ b/repository_dependencies.xml Tue Aug 01 07:57:15 2017 -0400
b
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
 <repositories description="This requires the HUMAnN2 data manager definition to install all required databases.">
     <repository changeset_revision="9c4ad82be5bd" name="data_manager_metaphlan2_database_downloader" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
-    <repository changeset_revision="1316375a8cbb" name="data_manager_humann2_database_downloader" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="854d9862a9f1" name="data_manager_humann2_database_downloader" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
 </repositories>
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diff -r 8ed686bd4229 -r ace84aac38ce static/images/731303924-page_DENITRIFICATION-PWY.png
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Binary file static/images/731303924-page_DENITRIFICATION-PWY.png has changed
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diff -r 8ed686bd4229 -r ace84aac38ce test-data/barplot1.png
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Binary file test-data/barplot1.png has changed
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diff -r 8ed686bd4229 -r ace84aac38ce test-data/barplot2.pdf
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Binary file test-data/barplot2.pdf has changed
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diff -r 8ed686bd4229 -r ace84aac38ce test-data/barplot3.svg
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/barplot3.svg Tue Aug 01 07:57:15 2017 -0400
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diff -r 8ed686bd4229 -r ace84aac38ce test-data/barplot4.png
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Binary file test-data/barplot4.png has changed
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diff -r 8ed686bd4229 -r ace84aac38ce test-data/hmp_pathabund.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hmp_pathabund.txt Tue Aug 01 07:57:15 2017 -0400
b
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0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\r\n'
b
diff -r 8ed686bd4229 -r ace84aac38ce test-data/rename_mapping
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rename_mapping Tue Aug 01 07:57:15 2017 -0400
b
@@ -0,0 +1,7 @@
+GO:0000015 GO1
+GO:0000049 GO2
+GO:0000179 GO3
+GO:0003697 GO4
+GO:0004594 GO5
+GO:0008137 GO6
+
b
diff -r 8ed686bd4229 -r ace84aac38ce test-data/rna_dna_norm-dna.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rna_dna_norm-dna.txt Tue Aug 01 07:57:15 2017 -0400
b
@@ -0,0 +1,7 @@
+# 1 2
+A 11 11
+A|1 10 10
+A|2 1 1
+D 5 10
+D|1 5 5
+D|2 0 5
b
diff -r 8ed686bd4229 -r ace84aac38ce test-data/rna_dna_norm-rna.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rna_dna_norm-rna.txt Tue Aug 01 07:57:15 2017 -0400
b
@@ -0,0 +1,7 @@
+# 1 2
+A 22 22
+A|1 20 20
+A|2 2 22
+R 10 20
+R|1 10 10
+R|2 0 10
b
diff -r 8ed686bd4229 -r ace84aac38ce test-data/strain_profiler-input.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/strain_profiler-input.txt Tue Aug 01 07:57:15 2017 -0400
b
@@ -0,0 +1,11 @@
+HEADERS 1 2 3
+A 10 10 10
+A|g1.s1 10 10 10
+A|g1.s2 0 10 10
+B 10 10 10
+B|g1.s1 10 10 10
+B|g1.s2 10 0 10
+C 10 10 10
+C|g1.s1 10 10 0
+C|g1.s2 10 10 0
+C|g1.s3 10 10 10