Mercurial > repos > florianbegusch > qiime2_suite
changeset 2:51025741f326 draft
Uploaded
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--- a/qiime2/.idea/workspace.xml Wed Jul 17 03:26:16 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,517 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<project version="4"> - <component name="ChangeListManager"> - <list default="true" id="b6f0e792-e8ea-43a1-9747-395b6f53af7f" name="Default Changelist" comment="" /> - <option name="EXCLUDED_CONVERTED_TO_IGNORED" value="true" /> - <option name="SHOW_DIALOG" value="false" /> - <option name="HIGHLIGHT_CONFLICTS" value="true" /> - <option name="HIGHLIGHT_NON_ACTIVE_CHANGELIST" value="false" /> - <option name="LAST_RESOLUTION" value="IGNORE" /> - </component> - <component name="FileEditorManager"> - <leaf SIDE_TABS_SIZE_LIMIT_KEY="300"> - <file pinned="false" current-in-tab="false"> - <entry file="file://$PROJECT_DIR$/qiime_sample-classifier_maturity-index.xml"> - <provider selected="true" editor-type-id="text-editor" /> - </entry> - </file> - <file pinned="false" current-in-tab="false"> - <entry file="file://$PROJECT_DIR$/qiime_feature-classifier_classify-sklearn.xml"> - 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</state> - </provider> - </entry> - <entry file="file://$PROJECT_DIR$/qiime_feature-table_merge-seqs.xml"> - <provider selected="true" editor-type-id="text-editor"> - <state relative-caret-position="360"> - <caret line="24" selection-start-line="24" selection-end-line="24" /> - </state> - </provider> - </entry> - <entry file="file://$PROJECT_DIR$/qiime_feature-table_merge-taxa.xml"> - <provider selected="true" editor-type-id="text-editor"> - <state relative-caret-position="360"> - <caret line="24" selection-start-line="24" selection-end-line="24" /> - </state> - </provider> - </entry> - <entry file="file://$PROJECT_DIR$/qiime_composition_ancom.xml"> - <provider selected="true" editor-type-id="text-editor"> - <state relative-caret-position="705"> - <caret line="47" column="65" selection-start-line="47" selection-start-column="65" selection-end-line="47" selection-end-column="65" /> - </state> - </provider> - </entry> - </component> - <component name="masterDetails"> - <states> - <state key="GlobalLibrariesConfigurable.UI"> - <settings> - <splitter-proportions> - <option name="proportions"> - <list> - <option value="0.2" /> - </list> - </option> - </splitter-proportions> - </settings> - </state> - <state key="JdkListConfigurable.UI"> - <settings> - <last-edited>1.8</last-edited> - <splitter-proportions> - <option name="proportions"> - <list> - <option value="0.2" /> - </list> - </option> - </splitter-proportions> - </settings> - </state> - <state key="ProjectJDKs.UI"> - <settings> - <last-edited>1.8</last-edited> - <splitter-proportions> - <option name="proportions"> - <list> - <option value="0.2" /> - </list> - </option> - </splitter-proportions> - </settings> - </state> - <state key="ProjectLibrariesConfigurable.UI"> - <settings> - <splitter-proportions> - <option name="proportions"> - <list> - <option value="0.2" /> - </list> - </option> - </splitter-proportions> - </settings> - </state> - </states> - </component> -</project> \ No newline at end of file
--- a/qiime2/qiime_composition_ancom.xml Wed Jul 17 03:26:16 2019 -0400 +++ b/qiime2/qiime_composition_ancom.xml Thu Jul 18 12:19:15 2019 -0400 @@ -9,6 +9,7 @@ --i-table=$itable +#if $input_files_mmetadatafile: #def list_dict_to_string(list_dict): #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name') #for d in list_dict[1:]: @@ -16,6 +17,7 @@ #end for #return $file_list #end def +#end if --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile) --m-metadata-column="$mmetadatacolumn"
--- a/qiime2/qiime_cutadapt_demux-paired.xml Wed Jul 17 03:26:16 2019 -0400 +++ b/qiime2/qiime_cutadapt_demux-paired.xml Thu Jul 18 12:19:15 2019 -0400 @@ -8,6 +8,7 @@ qiime cutadapt demux-paired --i-seqs=$iseqs + #def list_dict_to_string(list_dict): #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name') #for d in list_dict[1:]: @@ -16,8 +17,13 @@ #return $file_list #end def +#if $input_files_mforwardbarcodesfile: --m-forward-barcodes-file=$list_dict_to_string("$input_files_mforwardbarcodesfile") +#end if + +#if $input_files_mreversebarcodesfile: --m-reverse-barcodes-file=$list_dict_to_string("$input_files_mreversebarcodesfile") +#end if --m-forward-barcodes-column="$mforwardbarcodescolumn"
--- a/qiime2/qiime_cutadapt_demux-single.xml Wed Jul 17 03:26:16 2019 -0400 +++ b/qiime2/qiime_cutadapt_demux-single.xml Thu Jul 18 12:19:15 2019 -0400 @@ -12,6 +12,8 @@ --o-per-sample-sequences=opersamplesequences --o-untrimmed-sequences=ountrimmedsequences + +#if $input_files_mbarcodesfile: #def list_dict_to_string(list_dict): #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name') #for d in list_dict[1:]: @@ -19,8 +21,8 @@ #end for #return $file_list #end def - --m-barcodes-file=$list_dict_to_string("$input_files_mbarcodesfile") +#end if #if $perrorrate: --p-error-rate=$perrorrate
--- a/qiime2/qiime_demux_emp-paired.xml Wed Jul 17 03:26:16 2019 -0400 +++ b/qiime2/qiime_demux_emp-paired.xml Thu Jul 18 12:19:15 2019 -0400 @@ -11,6 +11,7 @@ --m-barcodes-column="$mbarcodescolumn" +#if $input_files_mbarcodesfile: #def list_dict_to_string(list_dict): #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name') #for d in list_dict[1:]: @@ -18,8 +19,8 @@ #end for #return $file_list #end def - --m-barcodes-file=$list_dict_to_string($input_files_mbarcodesfile) +#end if #if $pnogolayerrorcorrection:
--- a/qiime2/qiime_demux_emp-single.xml Wed Jul 17 03:26:16 2019 -0400 +++ b/qiime2/qiime_demux_emp-single.xml Thu Jul 18 12:19:15 2019 -0400 @@ -11,6 +11,7 @@ --m-barcodes-column="$mbarcodescolumn" +#if $input_files_mbarcodesfile: #def list_dict_to_string(list_dict): #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name') #for d in list_dict[1:]: @@ -18,8 +19,8 @@ #end for #return $file_list #end def - --m-barcodes-file=$list_dict_to_string($input_files_mbarcodesfile) +#end if #if $pnogolayerrorcorrection:
--- a/qiime2/qiime_diversity_adonis.xml Wed Jul 17 03:26:16 2019 -0400 +++ b/qiime2/qiime_diversity_adonis.xml Thu Jul 18 12:19:15 2019 -0400 @@ -10,6 +10,7 @@ --i-distance-matrix=$idistancematrix +#if $input_files_mmetadatafile: #def list_dict_to_string(list_dict): #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name') #for d in list_dict[1:]: @@ -17,10 +18,8 @@ #end for #return $file_list #end def - --m-metadata-file=$list_dict_to_string("$input_files_mmetadatafile") - - +#end if --p-formula="$pformula"
--- a/qiime2/qiime_diversity_alpha-group-significance.xml Wed Jul 17 03:26:16 2019 -0400 +++ b/qiime2/qiime_diversity_alpha-group-significance.xml Thu Jul 18 12:19:15 2019 -0400 @@ -10,6 +10,7 @@ --i-alpha-diversity=$ialphadiversity +#if $input_files_mmetadatafile: #def list_dict_to_string(list_dict): #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name') #for d in list_dict[1:]: @@ -17,8 +18,9 @@ #end for #return $file_list #end def +--m-metadata-file=$list_dict_to_string($input_files_mmetadatafile) +#end if ---m-metadata-file=$list_dict_to_string($input_files_mmetadatafile) --o-visualization=ovisualization ;
--- a/qiime2/qiime_diversity_beta-rarefaction.xml Wed Jul 17 03:26:16 2019 -0400 +++ b/qiime2/qiime_diversity_beta-rarefaction.xml Thu Jul 18 12:19:15 2019 -0400 @@ -28,6 +28,7 @@ --p-color-scheme=$pcolorscheme #end if +#if $input_files_mmetadatafile: #def list_dict_to_string(list_dict): #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name') #for d in list_dict[1:]: @@ -35,9 +36,8 @@ #end for #return $file_list #end def - --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile) - +#end if --o-visualization=ovisualization ;
--- a/qiime2/qiime_diversity_core-metrics-phylogenetic.xml Wed Jul 17 03:26:16 2019 -0400 +++ b/qiime2/qiime_diversity_core-metrics-phylogenetic.xml Thu Jul 18 12:19:15 2019 -0400 @@ -16,6 +16,8 @@ --p-n-jobs="$pnjobs" #end if + +#if $input_files_mmetadatafile: #def list_dict_to_string(list_dict): #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name') #for d in list_dict[1:]: @@ -23,8 +25,9 @@ #end for #return $file_list #end def +--m-metadata-file=$list_dict_to_string($input_files_mmetadatafile) +#end if ---m-metadata-file=$list_dict_to_string($input_files_mmetadatafile) --o-rarefied-table=orarefiedtable
--- a/qiime2/qiime_diversity_core-metrics.xml Wed Jul 17 03:26:16 2019 -0400 +++ b/qiime2/qiime_diversity_core-metrics.xml Thu Jul 18 12:19:15 2019 -0400 @@ -15,6 +15,7 @@ --p-n-jobs="$pnjobs" #end if +#if $input_files_mmetadatafile: #def list_dict_to_string(list_dict): #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name') #for d in list_dict[1:]: @@ -24,7 +25,7 @@ #end def --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile) - +#end if --o-rarefied-table=orarefiedtable --o-observed-otus-vector=oobservedotusvector
--- a/qiime2/qiime_emperor_biplot.xml Wed Jul 17 03:26:16 2019 -0400 +++ b/qiime2/qiime_emperor_biplot.xml Thu Jul 18 12:19:15 2019 -0400 @@ -18,8 +18,13 @@ #return $file_list #end def +#if $m_sample_metadatafile: --m-sample-metadata-file=$list_dict_to_string($m_sample_metadatafile) +#end if + +if $m_feature_metadatafile: --m-feature-metadata-file=$list_dict_to_string($m_feature_metadatafile) +#end if #if $pignoremissingsamples:
--- a/qiime2/qiime_feature-table_heatmap.xml Wed Jul 17 03:26:16 2019 -0400 +++ b/qiime2/qiime_feature-table_heatmap.xml Thu Jul 18 12:19:15 2019 -0400 @@ -9,6 +9,7 @@ --i-table=$itable + #if $input_files_mmetadatafile: #def list_dict_to_string(list_dict): #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
--- a/qiime2/qiime_feature-table_merge-seqs.xml Wed Jul 17 03:26:16 2019 -0400 +++ b/qiime2/qiime_feature-table_merge-seqs.xml Thu Jul 18 12:19:15 2019 -0400 @@ -7,6 +7,8 @@ <command><![CDATA[ qiime feature-table merge-seqs + +#if $input_files_idata: #def list_dict_to_string(list_dict): #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name') #for d in list_dict[1:]: @@ -15,6 +17,7 @@ #return $file_list #end def --i-data=$list_dict_to_string($input_files_idata) +#end if --o-merged-data=omergeddata
--- a/qiime2/qiime_feature-table_merge-taxa.xml Wed Jul 17 03:26:16 2019 -0400 +++ b/qiime2/qiime_feature-table_merge-taxa.xml Thu Jul 18 12:19:15 2019 -0400 @@ -7,6 +7,8 @@ <command><![CDATA[ qiime feature-table merge-taxa + +#if $input_files_idata: #def list_dict_to_string(list_dict): #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name') #for d in list_dict[1:]: @@ -15,6 +17,7 @@ #return $file_list #end def --i-data=$list_dict_to_string($input_files_idata) +#end if --o-merged-data=omergeddata
--- a/qiime2/qiime_feature-table_merge.xml Wed Jul 17 03:26:16 2019 -0400 +++ b/qiime2/qiime_feature-table_merge.xml Thu Jul 18 12:19:15 2019 -0400 @@ -7,6 +7,7 @@ <command><![CDATA[ qiime feature-table merge +#if $input_files_itables: #def list_dict_to_string(list_dict): #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name') #for d in list_dict[1:]: @@ -15,6 +16,7 @@ #return $file_list #end def --i-tables=$list_dict_to_string($input_files_itables) +#end if #if str($poverlapmethod) != 'None':
--- a/qiime2/qiime_feature-table_summarize.xml Wed Jul 17 03:26:16 2019 -0400 +++ b/qiime2/qiime_feature-table_summarize.xml Thu Jul 18 12:19:15 2019 -0400 @@ -9,6 +9,8 @@ --i-table=$itable + +#if $m_sample_metadatafile: #def list_dict_to_string(list_dict): #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name') #for d in list_dict[1:]: @@ -17,6 +19,8 @@ #return $file_list #end def --m-sample-metadata-file=$list_dict_to_string($m_sample_metadatafile) +#end if + --o-visualization=ovisualization ;
--- a/qiime2/qiime_gneiss_gradient-clustering.xml Wed Jul 17 03:26:16 2019 -0400 +++ b/qiime2/qiime_gneiss_gradient-clustering.xml Thu Jul 18 12:19:15 2019 -0400 @@ -11,6 +11,7 @@ --m-gradient-column="$mgradientcolumn" +#if $input_files_mgradientfile: #def list_dict_to_string(list_dict): #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name') #for d in list_dict[1:]: @@ -18,9 +19,8 @@ #end for #return $file_list #end def - --m-gradient-file=$list_dict_to_string($input_files_mgradientfile) - +#end if #if $pnoweighted: --p-no-weighted
--- a/qiime2/qiime_metadata_tabulate.xml Wed Jul 17 03:26:16 2019 -0400 +++ b/qiime2/qiime_metadata_tabulate.xml Thu Jul 18 12:19:15 2019 -0400 @@ -8,6 +8,7 @@ qiime metadata tabulate +#if $input_files_mmetadatafile: #def list_dict_to_string(list_dict): #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name') #for d in list_dict[1:]: @@ -16,6 +17,7 @@ #return $file_list #end def --m-input-file=$list_dict_to_string($input_files_minputfile) +#end if #if $ppagesize:
--- a/qiime2/qiime_quality-control_evaluate-composition.xml Wed Jul 17 03:26:16 2019 -0400 +++ b/qiime2/qiime_quality-control_evaluate-composition.xml Thu Jul 18 12:19:15 2019 -0400 @@ -10,6 +10,7 @@ --i-expected-features=$iexpectedfeatures --i-observed-features=$iobservedfeatures + #if $input_files_mmetadatafile: #def list_dict_to_string(list_dict): #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
--- a/qiime2/qiime_sample-classifier_classify-samples-ncv.xml Wed Jul 17 03:26:16 2019 -0400 +++ b/qiime2/qiime_sample-classifier_classify-samples-ncv.xml Thu Jul 18 12:19:15 2019 -0400 @@ -10,6 +10,7 @@ --i-table=$itable --m-metadata-column="$mmetadatacolumn" + #if $input_files_mmetadatafile: #def list_dict_to_string(list_dict): #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name') @@ -21,6 +22,7 @@ --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile) #end if + #if $pcv: --p-cv=$pcv #end if
--- a/qiime2/qiime_sample-classifier_maturity-index.xml Wed Jul 17 03:26:16 2019 -0400 +++ b/qiime2/qiime_sample-classifier_maturity-index.xml Thu Jul 18 12:19:15 2019 -0400 @@ -8,6 +8,7 @@ <![CDATA[ qiime sample-classifier maturity-index --i-table=$itable + #if $input_files_mmetadatafile: #def list_dict_to_string(list_dict): #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name') #for d in list_dict[1:]: @@ -16,7 +17,11 @@ #return $file_list #end def - --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile) --p-group-by="$pgroupby" --p-column="$pcolumn" --p-control="$pcontrol" + --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile) + #end fi + + + --p-group-by="$pgroupby" --p-column="$pcolumn" --p-control="$pcontrol" #set $pnjobs = '${GALAXY_SLOTS:-4}'