--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/add_pval_flags.xml	Fri Jun 18 20:23:19 2021 +0000
@@ -0,0 +1,140 @@
+<tool id="secimtools_add_pval_flags" name="Add Binary (0/1) -value Flags" version="@WRAPPER_VERSION@">
+  <description>using custom thresholds</description>
+  <macros>
+      <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements" />
+  <command detect_errors="exit_code"><![CDATA[
+    add_pval_flags.py
+    -de=$DE_Dataset
+    -id=$uniqID
+    -p=$pvalue
+    -t=$thresholds
+    -o=$output
+    -fl=$flags
+  ]]></command>
+  <inputs>
+    <param name="DE_Dataset" type="data" format="tabular" label="Select Dataset containing p-values from your history"/>
+    <param name="uniqID" type="text" size="30" value="" label="Unique FeatureID" help="Name of the column in your Dataset that contains unique FeatureIDs."/>
+    <param name="pvalue" type="text" size="30" value="" label="P-Value" help="Name of the column containing your p-values."/>
+    <param name="thresholds" type="text" size="30" value="0.1,0.05,0.01" label="P-Value Thresholds" help="Enter the threshold(s). P-values less than the given threshold(s) will be flagged with a 1. Separate more than 1 threshold value with a comma, no spaces allowed."/>
+  </inputs>
+  <outputs>
+    <data format="tabular" name="output" label="${tool.name} on ${on_string}: Output File"/>
+    <data format="tabular" name="flags" label="${tool.name} on ${on_string}: Flags File"/>
+  </outputs>
+  <tests>
+    <test>
+      <param name="DE_Dataset" value="limma_voom_gene_file_01fhl.tsv"/>
+      <param name="uniqID" value="UniqueID"/>
+      <param name="pvalue" value="P.Value"/>
+      <param name="thresholds" value="0.1,0.05,0.01"/>
+      <output name="output" file="add_flags_gene_output_file_01fhl.tsv"/>
+      <output name="flags" file="add_flags_gene_flags_file_01fhl.tsv"/>
+    </test>
+    <test>
+      <param name="DE_Dataset" value="limma_voom_metabolite_file_01fhl.tsv"/>
+      <param name="uniqID" value="UniqueID"/>
+      <param name="pvalue" value="P.Value"/>
+      <param name="thresholds" value="0.1,0.05,0.01"/>
+      <output name="output" file="add_flags_metabolite_output_file_01fhl.tsv"/>
+      <output name="flags" file="add_flags_metabolite_flags_file_01fhl.tsv"/>
+    </test>
+  </tests>
+  <help><![CDATA[
+
+
+**Tool Description**
+
+  This tool generates an indicator variable (0 or 1) to identify p-values below a user-specified threshold.  A “1” is used to indicate (flag)
+  p-values less than the indicated threshold p-value. The user can flag nominal p-values or p-values after correction for multiple testing.
+
+--------------------------------------------------------------------------------
+
+**INPUT**
+
+**Example of a dataset containing p-values**
+
+  +-----------+---------+---------+-----+
+  | FeatureID | P-value | FDR     | ... |
+  +===========+=========+=========+=====+
+  | one       | 2.02e-6 | 1.83e-6 | ... |
+  +-----------+---------+---------+-----+
+  | two       | 2.87e-5 | 0.0063  | ... |
+  +-----------+---------+---------+-----+
+  | three     | 0.001   | 0.19    | ... |
+  +-----------+---------+---------+-----+
+  | four      | 0.22    | 0.99    | ... |
+  +-----------+---------+---------+-----+
+  | ...       | ...     | ...     | ... |
+  +-----------+---------+---------+-----+
+
+**P-value**
+
+  Name of the column in your Dataset that contains p-values.
+
+**P-value Threshold**
+
+  P-values less than the threshold will be flagged with a 1. P-values greater than the threshold will be flagged with a 0.
+
+  **NOTE:** More than one threshold value is allowed. Separate flags will be generated for each threshold value.
+
+--------------------------------------------------------------------------------
+
+**OUTPUT**
+
+  Two output files are generated from the Add Binary (0/1) P-value Flags tool:
+
+**Output File.** A TSV file containing the same columns as the Input Dataset plus an additional column(s) containing 0/1 binary indicators for whether the P-value was less that the user-specified threshold.  The indicator columns are named by appending the user-specified threshold to 'Flag_' prefix (e.g. Flag_user-specified threshold, Flag_0.10).
+
+  +-----------+---------+---------+--------+-------------+-----+
+  | FeatureID | p-value | FDR     | Flag_0.2 | Flag_0.05 | ... |
+  +===========+=========+=========+==========+===========+=====+
+  | one       | 2.02e-6 | 1.83e-6 | 1        | 1         | ... |
+  +-----------+---------+---------+----------+-----------+-----+
+  | two       | 2.87e-5 | 0.0063  | 1        | 1         | ... |
+  +-----------+---------+---------+----------+-----------+-----+
+  | three     | 0.001   | 0.19    | 1        | 0         | ... |
+  +-----------+---------+---------+----------+-----------+-----+
+  | four      | 0.22    | 0.99    | 0        | 0         | ... |
+  +-----------+---------+---------+----------+-----------+-----+
+  | ...       | ...     | ...     | ...      | ...       | ... |
+  +-----------+---------+---------+----------+-----------+-----+
+
+**Flag Table.** A TSV file containing only the FeatureID column from the input dataset and the tool-generated binary indicator flags.
+
+  +-----------+----------+-----------+-----+
+  | FeatureID | Flag_0.2 | Flag_0.05 | ... |
+  +===========+==========+===========+=====+
+  | one       | 1        | 1         | ... |
+  +-----------+----------+-----------+-----+
+  | two       | 1        | 1         | ... |
+  +-----------+----------+-----------+-----+
+  | three     | 1        | 0         | ... |
+  +-----------+----------+-----------+-----+
+  | four      | 0        | 0         | ... |
+  +-----------+----------+-----------+-----+
+  | ...       | ...      | ...       | ... |
+  +-----------+----------+-----------+-----+
+
+  ]]>
+  </help>
+  <citations>
+    <citation type="bibtex">@ARTICLE{Kirpich17secimtools,
+    author = {Alexander S. Kirpich, Miguel Ibarra, Oleksandr Moskalenko, Justin M. Fear, Joseph Gerken, Xinlei Mi, Ali Ashrafi, Alison M. Morse, Lauren M. McIntyre},
+    title = {SECIMTools: A suite of Metabolomics Data Analysis Tools},
+    journal = {BMC Bioinformatics},
+    year = {in press}
+    }</citation>
+    <citation type="bibtex">@article{garcia2010paintomics,
+    title={Paintomics: a web based tool for the joint visualization of transcriptomics and metabolomics data},
+    author={Garc{\'\i}a-Alcalde, Fernando and Garc{\'\i}a-L{\'o}pez, Federico and Dopazo, Joaqu{\'\i}n and Conesa, Ana},
+    journal={Bioinformatics},
+    volume={27},
+    number={1},
+    pages={137--139},
+    year={2010},
+    publisher={Oxford University Press}
+    }</citation>
+  </citations>
+</tool>