diff --git a/docs/app.md b/docs/app.md
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@@ -0,0 +1,99 @@
+This module defines the command line interface.
+All commands have a ``--help`` option to get more info about them in the command line.
+
+
+## Print
+```bash
+robofish-io-print example.hdf5
+```
+Checking out the content of files.
+
+<small>
+
+```
+usage: robofish-io-print [-h] [--output_format {shape,full}] path
+
+This function can be used to print hdf5 files from the command line
+positional arguments:
+ path The path to a hdf5 file
+optional arguments:
+ -h, --help show this help message and exit
+ --output_format {shape,full}
+ Choose how datasets are printed, either the shapes or the full content is printed
+```
+
+</small>
+
+## Evaluate
+```bash
+robofish-io-evaluate *analysis_type* example.hdf5
+```
+Show some property of a file.
+
+
+<small>
+
+```
+usage: robofish-io-evaluate [-h] [--names NAMES [NAMES ...]] [--save_path SAVE_PATH]
+ {speed,turn,orientation,relative_orientation,distance_to_wall,tank_positions,trajectories,evaluate_positionVec,follow_iid} paths [paths ...]
+
+This function can be called from the commandline to evaluate files.
+Different evaluation methods can be called, which generate graphs from the given files.
+With the first argument 'analysis_type', the type of analysis is chosen.
+
+positional arguments:
+ {speed,turn,orientation,relative_orientation,distance_to_wall,tank_positions,trajectories,evaluate_positionVec,follow_iid}
+ The type of analysis.
+ speed - Evaluate the speed of the entities as histogram.
+ turn - Evaluate the turn angles of the entities as histogram.
+ orientation - Evaluate the orientations of the entities on a 2d grid.
+ relative_orientation - Evaluate the relative orientations of the entities as a histogram.
+ distance_to_wall - Evaluate the distances of the entities to the walls as a histogram.
+ tank_positions - Evaluate the positions of the entities as a heatmap.
+ trajectories - Evaluate the trajectories of the entities.
+ evaluate_positionVec - Evaluate the vectors pointing from the focal fish to the conspecifics as heatmap.
+ follow_iid - Evaluate the follow metric in respect to the inter individual distance (iid).
+ paths The paths to files or folders. Multiple paths can be given to compare experiments.
+
+optional arguments:
+ -h, --help show this help message and exit
+ --names NAMES [NAMES ...]
+ Names, that should be used in the graphs instead of the pahts.
+ --save_path SAVE_PATH
+ Filename for saving resulting graphics.
+```
+
+</small>
+
+## Trackviewer
+
+```bash
+robofish-trackviewer example.hdf5
+```
+
+The trackviewer is from a different repository. It was included in the install instructions.
+
+<small>
+
+```
+usage: robofish-trackviewer [-h] [--draw-labels] [--draw-view-vectors] [--far-plane FAR_PLANE] [--view-of-agents field of perception number of bins] [--view-of-walls field of perception number of bins]
+ [--view-of-walls-matches]
+ [trackset_file]
+
+View RoboFish tracks in a GUI.
+
+positional arguments:
+ trackset_file Path to HDF5 file containing the tracks to view
+
+optional arguments:
+ -h, --help show this help message and exit
+ --draw-labels Whether to draw labels inside the agents' outlines
+ --draw-view-vectors Whether to draw view vectors to the right of / below the trackfile
+ --far-plane FAR_PLANE
+ Maximum distance an agent can see
+ --view-of-agents field of perception number of bins
+ --view-of-walls field of perception number of bins
+ --view-of-walls-matches
+```
+
+</small>
\ No newline at end of file
diff --git a/docs/index.md b/docs/index.md
index 8e3fd95b1961ce15b4837d869f8b50d0747395d4..df674a31b092d893994a20961bf90ebcebbaf5ea 100644
--- a/docs/index.md
+++ b/docs/index.md
@@ -153,6 +153,7 @@ If you find bugs or get stuck somewhere, please text `Andi` on Mattermost or by
In the [Track Format Specification](https://git.imp.fu-berlin.de/bioroboticslab/robofish/track_format/uploads/f76d86e7a629ca38f472b8f23234dbb4/RoboFish_Track_Format_-_1.0.pdf) and in this package there are more possibilities, we don't describe explicitly here. If you want to use any of the following features, please ask Andi:
Built in robofish.io and not described:
+
- Multiple sampling frequencies
- Timestamps per timestep
- Calendar points
@@ -160,6 +161,7 @@ Built in robofish.io and not described:
- Obstacles
Planned in Track Format but not implemented:
+
- 3D Tracks
diff --git a/src/robofish/io/app.py b/src/robofish/io/app.py
index fc6fee0f27766b179fa494547b67cee736cd7083..e31e9ca38a8584312ec8250c6bb733a55b03c479 100644
--- a/src/robofish/io/app.py
+++ b/src/robofish/io/app.py
@@ -1,10 +1,10 @@
# -*- coding: utf-8 -*-
+"""
+.. include:: ../../../docs/app.md
+"""
+
# -----------------------------------------------------------
-# Functions available to be used in the commandline to show and validate hdf5
-# according to the Robofish track format (1.0 Draft 7). The standard is
-# available at https://git.imp.fu-berlin.de/bioroboticslab/robofish/track_format
-#
# Dec 2020 Andreas Gerken, Berlin, Germany
# Released under GNU 3.0 License
# email andi.gerken@gmail.com