--- a/qiime2/merge_feature_table_and_taxonomy.xml	Wed May 23 10:29:25 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,30 +0,0 @@
-<?xml version="1.0" ?>
-<tool id="merge_feature_table_and_taxonomy" name="merge feature table and taxonomy" version="2018.4">
-	<description>- Merge features and taxonomy into a single biom file.</description>
-	<requirements>
-		<requirement type="package" version="2018.4">qiime2</requirement>
-	</requirements>
-	<command>
-mkdir out;
-
-qiime tools export --output-dir out $taxonomy_qza;
-qiime tools export --output-dir out $biom_qza;
-
-sed -i '1s;^;#;' out/*.tsv;
-sed -i 's/Confidence/confidence/g' out/*.tsv;
-sed -i 's/Taxon/taxonomy/g' out/*.tsv;
-sed -i 's/Feature ID/OTU ID/g' out/*.tsv;
-
-biom add-metadata -i out/*.biom -o table_with_sample_metadata.biom --observation-metadata-fp out/*.tsv
-;
-mv *.biom $biom_and_tax_merged</command>
-	<inputs>
-		<param label="Feature table" name="biom_qza" type="data" format="qza,no_unzip.zip" collection_type="list"/>
-		<param label="Taxonomy" name="taxonomy_qza" type="data" format="qza,no_unzip.zip"/>
-	</inputs>
-	<outputs>
-		<data format="biom2" label="${tool.name} on ${on_string}: biom_and_tax_merged.biom" name="biom_and_tax_merged"/>
-	</outputs>
-	<help>
-</help>
-</tool>

--- a/qiime2/qiime_composition_add-pseudocount.xml	Wed May 23 10:29:25 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,51 +0,0 @@
-<?xml version="1.0" ?>
-<tool id="qiime_composition_add-pseudocount" name="qiime composition add-pseudocount" version="2018.2">
-	<description> - Add pseudocount to table</description>
-	<requirements>
-		<requirement type="package" version="2018.2">qiime2</requirement>
-	</requirements>
-	<command><![CDATA[
-  
-  qiime composition add-pseudocount --i-table=$itable
-  
-  #if $ppseudocount:
-   --p-pseudocount=$ppseudocount
-  #end if
-
-  #if str($cmdconfig) != 'None':
-   --cmd-config=$cmdconfig
-  #end if
-  
-  --o-composition-table=ocompositiontable
-  ;
-  cp ocompositiontable.qza $ocompositiontable
-
-]]></command>
-	<inputs>
-		<param format="qza,no_unzip.zip" label="--i-table: FeatureTable[Frequency] - The feature table to which pseudocounts should be added.  [required]" name="itable" optional="False" type="data"/>
-		<param label="--p-pseudocount: The value to add to all counts in the feature table.  [default: 1]" name="ppseudocount" optional="True" type="integer" value="1"/>
-		<param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
-	</inputs>
-	<outputs>
-		<data format="qza" label="${tool.name} on ${on_string}: compositiontable.qza" name="ocompositiontable"/>
-	</outputs>
-	<help><![CDATA[
-Add pseudocount to table
-------------------------
-
-Increment all counts in table by pseudocount.
-
-Parameters
-----------
-table : FeatureTable[Frequency]
-    The feature table to which pseudocounts should be added.
-pseudocount : Int, optional
-    The value to add to all counts in the feature table.
-
-Returns
--------
-composition_table : FeatureTable[Composition]
-    The resulting feature table.
- ]]>
-</help>
-</tool>