diff secimtools/standardized_euclidean_distance.xml @ 2:caba07f41453 draft default tip

"planemo upload for repository https://github.com/secimTools/SECIMTools/tree/main/galaxy commit 498abad641099412df56f04ff6e144e4193bbc34-dirty"

--- a/secimtools/standardized_euclidean_distance.xml	Mon Mar 08 22:04:06 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,116 +0,0 @@
-<tool id="secimtools_standardized_euclidean_distance" name="Standardized Euclidean Distance (SED)" version="@WRAPPER_VERSION@">
-    <description>calculated for the data.</description>
-    <macros>
-        <import>macros.xml</import>
-    </macros>
-    <expand macro="requirements" />
-    <command detect_errors="exit_code"><![CDATA[
-standardized_euclidean_distance.py
---input $input
---design $design
---ID $uniqID
---fig $plot
---SEDtoMean $out1
---SEDpairwise $out2
-
-#if $group
-    --group $group
-#end if
-#if $levels
-	--levels $levels
-#end if
-#if $p
-    --per $p
-#end if
-
-#if $order
-    --order $order
-#end if
-    ]]></command>
-    <inputs>
-        <param name="input" type="data" format="tabular" label="Wide Dataset" help="Input dataset in wide format and tab separated. If file not tab separated see TIP below."/>
-        <param name="design" type="data" format="tabular" label="Design File" help="Design file tab separated. Note you need a 'sampleID' column. If not tab separated see TIP below."/>
-        <param name="uniqID" type="text" size="30" value="" label="Unique Feature ID" help="Name of the column in your Wide Dataset that has unique Feature IDs."/>
-        <param name="group" type="text" size="30" label="Group/Treatment [Optional]" help="Name of the column in your Design File that contains group classifications." />
-        <param name="order" type="text" size="30" label="Input Run Order Name [Optional]" help="Enter the name of the column containing the order samples were run. Spelling and capitalization must be exact." />
-        <param name="levels" type="text" size="30" label="Additional groups to separate by [Optional]" help="Enter additional group(s) name(s). Spelling and capitalization must be exact. If more than one group separate with a ','." />
-        <param name="p" type="float" value= "0.95" size="6" label="Threshold" help="Threshold for standard distribution, specified as percentile. Default = 0.95." />
-    </inputs>
-    <outputs>
-        <data format="pdf" name="plot" label="${tool.name} on ${on_string}: Plot" />
-        <data format="tabular" name="out1" label="${tool.name} on ${on_string}: SEDtoMean" />
-        <data format="tabular" name="out2" label="${tool.name} on ${on_string}: SEDpairwise" />
-    </outputs>
-    <tests>
-        <test>
-            <param name="input"  value="ST000006_data.tsv"/>
-            <param name="design" value="ST000006_design.tsv"/>
-            <param name="uniqID" value="Retention_Index" />
-            <param name="group"  value="White_wine_type_and_source" />
-            <output name="plot"  value="ST000006_standardized_euclidean_distance_figure.pdf" compare="sim_size" delta="50000" />
-            <output name="out1"  file="ST000006_standardized_euclidean_distance_to_mean.tsv" />
-            <output name="out2"  file="ST000006_standardized_euclidean_distance_pairwise.tsv" />
-        </test>
-    </tests>
-    <help><![CDATA[
-
-@TIP_AND_WARNING@
-
-**Tool Description**
-
-The tool is designed to identify samples that are different using the standardized Euclidian distance (SED) between samples.
-The tool estimates the variance of features and calculates the SED between each pair of samples in addition to the SED between each sample and the estimated mean.
-If a group or treatment variable is provided, then the same distance plots are generated for each group and for all samples together.
-
-**NOTE:** Groups with less than three samples will be excluded from the analysis.
-
-
-
-**Input**
-
-    - Two input datasets are required.
-
-@WIDE@
-
-**NOTE:** The sample IDs must match the sample IDs in the Design File
-(below). Extra columns will automatically be ignored.
-
-@METADATA@
-
-@UNIQID@
-
-@GROUP_OPTIONAL@
-
-    - **Warning:** All groups must contain 3 or more samples.
-
-
-@RUNORDER_OPTIONAL@
-
-**Additional groups to separate by [Optional]**
-
-    - Enter group(s) name(s). Spelling and capitalization must be exact. If more than one group, separate with commas.
-    - **Warning:** All groups must contain 3 or more samples.
-    - **NOTE:** Groups with one element will be excluded from the analysis.
-
-
-**Percentile cutoff**
-
-- The percentile cutoff for standard distributions. The default is 0.95.
-
---------------------------------------------------------------------------------
-
-**Output**
-
-The tool outputs three different files:
-
-(1) a TSV file that contains a n x n matrix (where n is the number computed samples) of the pairwise distances between the samples.
-If the Group/Treatment [Optional] variable is specified, the distances will be computed within groups.
-
-(2) A PDF file containing:
-(i) Boxplots of the distribution of distances.  The distances are computed between samples in the group and summarized as boxplots.
-The outliers (blue dots), means (red squares) and median (blue bars) of the distances are presented for each sample within the group.
-(ii) 2D scatter plots that show distances computed pairwise within the group
-
-    ]]></help>
-    <expand macro="citations"/>
-</tool>