Please help me with the inputs to be given to run the above specified tool. I am working with drug discovery and trying to check the protein-lead compound distance. The tool runs fine, but resulted like this:
| Column 1 | Column 2 |
|---|---|
| 0 | 0.0 |
| 1 | 0.0 |
| 2 | 0.0 |
| 3 | 0.0 |
| 4 | 0.0 |
| 5 | 0.0 |
| 6 | 0.0 |
| 7 | 0.0 |
| 8 | 0.0 |
| 9 | 0.0 |
| 10 | 0.0 |
| 11 | 0.0 |
| 12 | 0.0 |
Hello @swathin
The issue could be with the content of the inputs or the parameters used. We can help with protocol here, including the upstream step when preparing the inputs, and with matching up command-line parameters to tool form options. To do this, we’ll need to see this job and the current upstream steps that created your inputs – you can do this by generating and pasting back a share link to your history. If you are already following some tutorial, or using a workflow, links to those can help as well.
You can also explore yourself! Below are some ideas. 
Please let us know if we can help more or if you are able to solve the problem! It is difficult to guess more without reviewing the details closer.
The output is one place to look and the job Details view is another (follow the i-icon on the output dataset). The job logs in this view are from the Galaxy wrapper around the tool and includes messages from the original underlying tool. These runtime logs (when generated) can include useful metrics, not just details about how the job processed.
Does your job include any messages here?
We have an example in this GTN tutorial (following the links on the tool form, scroll down to find)
Galaxy Training! Tutorials for Distance Analysis: Time series using MDAnalysis → Hands-on: Analysis of molecular dynamics simulations / Analysis of molecular dynamics simulations / Computational chemistryTutorials include simple but representative sample data and (usually!) a workflow. Running the data through the workflow to create an example Answer Key history for comparison is the starting place. This suite of data can be useful to experiment with other tools too!
Tool in Galaxy work about the same as they do when run directly. This means that while the tool form may have some short help, the original guide is the definitive source when reviewing how the tool is performing the scientific calculations and what those data represent. Tool forms may include a link to these external resources in the upper help section and the links to the dependency packages near the bottom will supplement.
bio.tools link for mdanalysis → https://bio.tools/mdanalysisThis seems to be the most relevant interpretation in the guide, given what you shared:
Blocks of low RMSD values anywhere indicate that the two trajectories are sampling similar states.
Figuring out the “why” for this type of result is where I would suggest starting. There could be something as simple as a sample mixup, or format issue (file, IDs involved), or there could be a more complex protocol issue with this or the upstream data preparation steps. Once those technical issues are eliminated, then the result can be interpreted scientifically: the current protocol/parameters applied to the current data may actually not have any measurable differences! Modifying the protocol or parameters could be explored next.
While the instructions are for running the tool directly or inside of a Jupyter container (which you could also do in Galaxy!), the primary options should be transferable onto the web tool form and datasets involved. Using the GTN tutorial data is one way to explore the method using simple inputs with somewhat known results for your comparison.
Let me check the contents of the input.
Thank you for providing the usage guides @jennaj