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

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

--- a/secimtools/summarize_flags.xml	Mon Mar 08 22:04:06 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,70 +0,0 @@
-<tool id="secimtools_summarize_flags" name="Summarize Flags in a Flag File" version="@WRAPPER_VERSION@">
-    <description></description>
-    <macros>
-        <import>macros.xml</import>
-    </macros>
-    <expand macro="requirements" />
-    <command><![CDATA[
-summarize_flags.py
---flags $flags
---ID $uniqID
---outSummary $summaryFlags
-    ]]></command>
-    <inputs>
-        <param name="flags" type="data" format="tabular" label="Flag File"
-               help="Input flagged dataset containing the flag value for each feature."/>
-        <param name="uniqID" type="text" size="30" value="" label="Unique Feature ID"
-               help="Name of the column in your Wide Dataset that has unique Feature IDs."/>
-    </inputs>
-    <outputs>
-        <data name="summaryFlags" format="tabular" label="${tool.name} on ${on_string}"/>
-    </outputs>
-    <tests>
-        <test>
-            <param name="flags"   value="ST000006_lasso_enet_var_select_flags.tsv"/>
-            <param name="uniqID"  value="Retention_Index" />
-            <output name="summaryFlags" file="ST000006_summarize_flags_outSummary.tsv" />
-        </test>
-    </tests>
-    <help><![CDATA[
-
-@TIP_AND_WARNING@
-
-**Tool Description**
-
-Summary of the Flags
-
-This tool takes a wide format flag file and summarizes the information about the flags.
-The flag summary includes, for each feature:
-(i) the sum of the flags,
-(ii) the mean of the flags,
-(iii) an indicator if at least one of the original flags had a value of 1 and
-(iv) a second indicator if all of the original flags had a value of 1.
-
---------------------------------------------------------------------------------
-
-**Input**
-
-    - One input dataset is required.
-
-@FLAGS@
-
-@UNIQID@
-
---------------------------------------------------------------------------------
-
-**Output**
-
-This tool will output a TSV file containing all original input flag data with four additional columns containing the flag summaries.
-
-The four additional columns are:
-
-(i) a column with the sum of the flags,
-(ii) a column with the flag means, and
-(iii) a flag indicator column if at least one of the original flags had a value of 1
-(iv) a second flag indicator column if all of the original flags had a value of 1
-
-
-    ]]></help>
-    <expand macro="citations"/>
-</tool>