Mercurial > repos > oinizan > frogs
diff frogsfunc_pathways.xml @ 21:74a9b83110a7 draft
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit f481f7af0d70c862c493d55f386b375e7f968c5c-dirty
| author | oinizan |
|---|---|
| date | Thu, 30 Mar 2023 06:09:01 +0000 |
| parents | ca1e9adbde51 |
| children | 57824202c333 |
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--- a/frogsfunc_pathways.xml Fri Mar 10 14:03:08 2023 +0000 +++ b/frogsfunc_pathways.xml Thu Mar 30 06:09:01 2023 +0000 @@ -15,7 +15,7 @@ # You should have received a copy of the GNU General Public License # along with this program. If not, see <http://www.gnu.org/licenses/>. --> -<tool id="FROGSFUNC_step4_pathways" name="FROGSFUNC_step4_pathways" version= "@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> +<tool id="FROGSFUNC_step4_pathways" name="FROGSFUNC_3_pathways" version= "@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> <description>Calculates pathway abundances in each sample. </description> <macros> @@ -35,17 +35,11 @@ --normalisation #end if --map $map_file.value - - #if $category.value == "16S" - #if $map_file.fields.name == "Kegg" - --no-regroup - #end if - #end if --summary $summary_file </command> <inputs> <!-- Input files --> - <param argument="--input-file" format="tsv" name="input_file" type="data" label="Function abundance file" help="TSV function abundances table from FROGSFUNC_step3_function tool, frogsfunc_functions_unstrat.tsv (unstratified table)." optional="false"/> + <param argument="--input-file" format="tsv" type="data" label="Function abundance file" help="TSV function abundances table from FROGSFUNC_2_functions tool, FROGSFUNC_2_functions_unstrat_EC.tsv for Metacyc database or FROGSFUNC_2_functions_unstrat_KO.tsv for Kegg database (unstratified table)." optional="false"/> <!-- References --> <param name="category" type="select" label="Taxonomic marker" help="Taxonomic marker of interest." multiple="false" display="radio"> @@ -56,7 +50,7 @@ <validator type="no_options" message="A built-in database is not available" /> </options> </param> - <param name="map_file" type='select' label="Pathway reference" help="For 16S marker, choose Metacyc or KEGG in accordance with your choice in the FROGSFUNC_step2_copynumbers tool. For ITS or 18S marker, Metacyc is the only valid option." optional="false" multiple='false' display='radio'> + <param name="map_file" type='select' label="Pathway reference" help="For 16S marker, choose Metacyc or KEGG in accordance with your choice in the FROGSFUNC_1_placeseqs_copynumbers tool. For ITS or 18S marker, Metacyc is the only valid option." optional="false" multiple='false' display='radio'> <options from_data_table="frogs_picrust2_pathway_map"> <column name='name' index='1'/> <column name='value' index='3'/> @@ -70,7 +64,7 @@ </inputs> <outputs> <data format="html" name="summary_file" label="${tool.name}: report.html" from_work_dir="report.html"/> - <data format="tsv" name="abund" label="${tool.name}: frogsfunc_pathways_unstrat.tsv" from_work_dir="frogsfunc_pathways_unstrat.tsv"/> + <data format="tsv" name="abund" label="${tool.name}: frogsfunc_pathways_unstrat.tsv" from_work_dir="frogsfunc_pathways_unstrat.tsv"/> </outputs> <tests> @@ -91,10 +85,10 @@ What it does -FROGSFUNC_step4_pathway is the last step of `PICRUSt2 <https://github.com/picrust/picrust2>`_. This script infers MetaCyc/KEGG pathway abundances based on EC/KO number abundances. +**FROGSFUNC_3_pathways** is the last step of `PICRUSt2 <https://github.com/picrust/picrust2>`_. This script infers MetaCyc/KEGG pathway abundances based on **EC** or **KO** number abundances. - - Regroups EC/KO numbers to MetaCyc/KEGG reactions. - - Infers which MetaCyc/KEGG pathways are present based on these reactions with `MinPath <http://omics.informatics.indiana.edu/MinPath/>`_. + - Regroups EC or KO numbers to MetaCyc or KEGG reactions, depending of the unstrat abundances input file. + - Infers which MetaCyc or KEGG pathways are present based on these reactions with `MinPath <http://omics.informatics.indiana.edu/MinPath/>`_. - Calculates and returns the abundance of pathways identified as present. .. class:: infomark page-header h2 @@ -105,23 +99,23 @@ Input -**Function prediction abundance file**: +**-Function prediction abundance file (EC or KO)-**: - TSV function abundances table from FROGSFUNC_step3_function tool, frogsfunc_functions_unstrat.tsv (unstratified table). + TSV function abundances table from FROGSFUNC_2_functions tool, frogsfunc_functions_unstrat_EC.tsv or frogsfunc_functions_unstrat_KO.tsv (unstratified table). -**Taxonomic marker:** +**-Taxonomic marker-**: - Output table of predicted marker gene copy numbers per sequence from FROGSFUNC_step2_copynumbers tool. (frogsfunc_copynumbers_marker.tsv) + Output table of predicted marker gene copy numbers per sequence from FROGSFUNC_1_placeseqs tool. (frogsfunc_marker.tsv) -**Pathway reference:** +**-Pathway reference-**: Mapping of pathways to reactions. - - For 16S marker, choose Metacyc or KEGG in accordance with your choice in the FROGSFUNC_step2_copynumbers tool. If you want both, run this tool twice. + - For 16S marker, choose Metacyc or KEGG in accordance with your choice in the FROGSFUNC_2_functions tool. If you want both, run this tool twice. - For ITS or 18S marker, Metacyc is the only valid option. -**Do you want to normalize the final output table ?**: +**-Do you want to normalize the final output table ?-**: If this option is set, the pathway abundances file (frogsfunc_functions_unstrat.tsv) is normalized: values are divided by sum of columns, then multiplied by 10^6 (Count Per Million values). @@ -133,16 +127,14 @@ Outputs -**HTML report**: +**-HTML report-**: The HTML file summarizes information about pathway abundances within each sample. .. image:: FROGS_frogsfunc_pathways_sunburst.png - - -**Pathways abundances tables - unstratified**: +**-Pathways abundances tables - unstratified-**: It is the pathways abundance predictions of metagenome, per sample. (frogsfunc_pathways_unstrat.tsv)