# HG changeset patch
# User mvdbeek
# Date 1540569486 14400
# Node ID 7f827a8e4ec5c742224dfdda2fea009a848c423a

planemo upload for repository https://github.com/bardin-lab/damid_galaxy_tools commit c753dd4f3e1863aae7ba45dcc7efdf6937b03542-dirty

diff -r 000000000000 -r 7f827a8e4ec5 consecutive_peaks.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/consecutive_peaks.py	Fri Oct 26 11:58:06 2018 -0400
@@ -0,0 +1,34 @@
+import click
+import numpy as np
+import pandas as pd
+
+SHIFTED_PADJ_COLUMN = 'shifted'
+CONSECUTIVE_MAX = 'consecutive_max'
+PEAKS_PER_GROUP = 'peaks_per_group'
+
+
+@click.command()
+@click.argument('input_file', type=click.Path(exists=True))
+@click.argument('output_file', type=click.Path())
+@click.argument('padj_column', default=8)
+@click.argument('groupby_column', default=9)
+@click.argument('add_number_of_peaks', default=True)
+def determine_consecutive_peaks(input_file, output_file, padj_column, groupby_column, add_number_of_peaks):
+    """Finds the two lowest consecutives peaks for a group and reports"""
+    df = pd.read_csv(input_file, sep='\t', header=None)
+    grouped = df.groupby(groupby_column, sort=False)
+    if add_number_of_peaks:
+        df[PEAKS_PER_GROUP] = grouped[groupby_column].transform(np.size)
+    df[SHIFTED_PADJ_COLUMN] = grouped[8].shift()
+    df[CONSECUTIVE_MAX] = df[[padj_column, SHIFTED_PADJ_COLUMN]].max(axis=1)
+    grouped = df.groupby(groupby_column, sort=False)
+    idx = grouped[CONSECUTIVE_MAX].transform(min)  # index of groupwise consecutive minimum
+    new_df = df[df[CONSECUTIVE_MAX] == idx]
+    new_df.sort_values(by=CONSECUTIVE_MAX)
+    new_df[padj_column].replace(new_df[CONSECUTIVE_MAX])
+    new_df = new_df.drop(labels=[CONSECUTIVE_MAX, SHIFTED_PADJ_COLUMN], axis=1)
+    new_df.to_csv(output_file, sep='\t', header=None, na_rep="NaN")
+
+
+if __name__ == '__main__':
+    determine_consecutive_peaks()
diff -r 000000000000 -r 7f827a8e4ec5 consecutive_peaks.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/consecutive_peaks.xml	Fri Oct 26 11:58:06 2018 -0400
@@ -0,0 +1,27 @@
+<tool id="consecutive_peaks" name="Consecutive peaks" version="0.1.0">
+    <requirements>
+        <requirement type="package" version="7.0">click</requirement>
+        <requirement type="package" version="0.23.4">pandas</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+python '$__tool_directory__/consecutive_peaks.py' '$input_file' '$output_file'
+    ]]></command>
+    <inputs>
+       <param name="input_file" type="data" format="tabular" label="Input file" help="file containing peaks and genes"/>
+       <param name="padj_column" type="data_column" data_ref="input_file" value="c8" label="Column containing padj value"/>
+       <param name="groupby" type="data_column" data_ref="input_file" value="c9" label="Group values by this column" help="Usually gene id."/>
+    </inputs>
+    <outputs>
+        <data name="output_file" format_source="input_file"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_file" value="deseq2_peaks.bed"/>
+            <output name="output_file" value="grouped.bed"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+Can be used to get the lowest p.adj for 2 consecutive peaks in a gene.
+The reported p.adj is the higher p.adj of the 2 consecutive peaks.
+    ]]></help>
+</tool>
diff -r 000000000000 -r 7f827a8e4ec5 test-data/deseq2_peaks.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/deseq2_peaks.bed	Fri Oct 26 11:58:06 2018 -0400
@@ -0,0 +1,40 @@
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diff -r 000000000000 -r 7f827a8e4ec5 test-data/grouped.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/grouped.bed	Fri Oct 26 11:58:06 2018 -0400
@@ -0,0 +1,9 @@
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