Mercurial > repos > iuc > qiime_filter_otus_from_otu_table

diff filter_otus_from_otu_table.xml @ 5:e84a31935a8b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
author iuc
date Sat, 05 Aug 2017 07:31:22 -0400
parents 8824c27efae2
children 9db0d2cf4451
line wrap: on
line diff
--- a/filter_otus_from_otu_table.xml	Mon Jul 10 16:40:19 2017 -0400
+++ b/filter_otus_from_otu_table.xml	Sat Aug 05 07:31:22 2017 -0400
@@ -1,50 +1,50 @@
-<tool id="qiime_filter_otus_from_otu_table" name="Filter otus from otu table" version="@WRAPPER_VERSION@.0">
-    <description>Filter OTUs from an OTU table based on their observation counts or identifier</description>
+<tool id="qiime_filter_otus_from_otu_table" name="Filter OTUs from an OTU table" version="@WRAPPER_VERSION@.0">
+    <description> based on their observation counts or identifier (filter_otus_from_otu_table)</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements"/>
     <version_command>filter_otus_from_otu_table.py --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
-        filter_otus_from_otu_table.py
-            --input_fp '$input_fp'
-            --output_fp '$output_fp'
-            #if $min_count != '':
-                --min_count '$min_count'
-            #end if
-            #if $min_count_fraction != '':
-                --min_count_fraction '$min_count_fraction'
-            #end if
-            #if $max_count != '':
-                --max_count '$max_count'
-            #end if
-            #if $min_samples != '':
-                --min_samples '$min_samples'
-            #end if
-            #if $max_samples != '':
-                --max_samples '$max_samples'
-            #end if
-            #if $id_filtering_condition.id_filtering_switch == 'yes':
-                --otu_ids_to_exclude_fp '$id_filtering_condition.otu_ids_to_exclude_fp'
-                $id_filtering_condition.negate_ids_to_exclude
-            #end if
+filter_otus_from_otu_table.py
+    --input_fp '$input_fp'
+    --output_fp '$output_fp'
+    #if $min_count != '':
+        --min_count '$min_count'
+    #end if
+    #if $min_count_fraction != '':
+        --min_count_fraction '$min_count_fraction'
+    #end if
+    #if $max_count != '':
+        --max_count '$max_count'
+    #end if
+    #if $min_samples != '':
+        --min_samples '$min_samples'
+    #end if
+    #if $max_samples != '':
+        --max_samples '$max_samples'
+    #end if
+    #if $id_filtering_condition.id_filtering_switch == 'yes':
+        --otu_ids_to_exclude_fp '$id_filtering_condition.otu_ids_to_exclude_fp'
+        $id_filtering_condition.negate_ids_to_exclude
+    #end if
     ]]></command>
     <inputs>
-        <param argument="--input_fp" type="data" format="biom1" optional="False" label="Input OTU table" help="The input otu table filepath in biom format"  />
-        <param argument="--min_count" type="integer" value="0" optional="True" label="Minimum total observation count of an otu for that otu to be retained" />
-        <param argument="--min_count_fraction" type="float" value="0.0" optional="True" label="Fraction of the total observation (sequence) count to apply as the minimum total observation count of an otu for that otu to be retained" help="This is a fraction (float), not a percentage, so if you want to filter to 1%, you need to use 0.01 as value here" />
-        <param argument="--max_count" type="integer" value="" optional="True" label="Maximum total observation count of an otu for that otu to be retained" />
-        <param argument="--min_samples" type="integer" value="0" optional="True" label="Minimum number of samples an OTU must be observed in for that otu to be retained" />
-        <param argument="--max_samples" type="integer" value="" optional="True" label="Maximum number of samples an OTU must be observed in for that otu to be retained" />
+        <param argument="--input_fp" type="data" format="biom1" optional="false" label="Input OTU table" help="The input otu table filepath in biom format"  />
+        <param argument="--min_count" type="integer" value="0" optional="true" label="Minimum total observation count of an otu for that otu to be retained" />
+        <param argument="--min_count_fraction" type="float" value="0.0" optional="true" label="Fraction of the total observation (sequence) count to apply as the minimum total observation count of an otu for that otu to be retained" help="This is a fraction (float), not a percentage, so if you want to filter to 1%, you need to use 0.01 as value here" />
+        <param argument="--max_count" type="integer" value="" optional="true" label="Maximum total observation count of an otu for that otu to be retained" />
+        <param argument="--min_samples" type="integer" value="0" optional="true" label="Minimum number of samples an OTU must be observed in for that otu to be retained" />
+        <param argument="--max_samples" type="integer" value="" optional="true" label="Maximum number of samples an OTU must be observed in for that otu to be retained" />
         <conditional name="id_filtering_condition">
-            <param name="id_filtering_switch" type="select" label="Do you want to exclude a predefined list of OTUs from the OTU table ?" >
+            <param name="id_filtering_switch" type="select" label="Do you want to exclude a predefined list of OTUs from the OTU table?" >
                 <option value="no" selected="true">No</option>
                 <option value="yes">Yes</option>
             </param>
             <when value="no"/>
             <when value="yes">
-                <param argument="--otu_ids_to_exclude_fp" type="data" format="fasta,txt" optional="False"  label="Filtering by ID / Chimera filtering - Input text/Fasta file containing a list of OTU ids to exclude" help="The selected file can be a text file with one id per line, a text file where id is the first value in a tab-separated line, or can be a fasta file (extension must be .fna or .fasta)" />
-                <param argument="--negate_ids_to_exclude" type="boolean" label="Do you want to reverse the filtering by ID / Chimera filtering ?" truevalue="--negate_ids_to_exclude" falsevalue="" checked="False" help="When this parameter is set to yes, then only the OTUs listed in the file passed to the --otu_ids_to_exclude_fp parameters will be kept in the output biom file" />
+                <param argument="--otu_ids_to_exclude_fp" type="data" format="fasta,txt" label="Filtering by ID / Chimera filtering - Input text/Fasta file containing a list of OTU ids to exclude" help="The selected file can be a text file with one id per line, a text file where id is the first value in a tab-separated line, or can be a fasta file (extension must be .fna or .fasta)" />
+                <param argument="--negate_ids_to_exclude" type="boolean" truevalue="--negate_ids_to_exclude" falsevalue="" checked="false" label="Do you want to reverse the filtering by ID / Chimera filtering ?" help="When this parameter is set to yes, then only the OTUs listed in the file passed to the --otu_ids_to_exclude_fp parameters will be kept in the output biom file" />
             </when>
         </conditional>
     </inputs>