galaxy wrapper for the scp tool

[KristinaGomoryova]

This PR includes the galaxy wrapper for the scp, an R package for the mass spectrometry-based single cell data analysis. All the package functionality is built into a one tool, where user can pre-define all settings. Several graphs are outputted.

[hechth]

@bgruening the tests are passing and seem fine with conda but it doesn't work with the biocontainers for some reason. It can't find the Rscript command - do you have some idea of what is going on there?

[bgruening]

Where do you see the error with RScript. On CI the error is a different diff on Test 2.
(I'm a bit worried about the strange symbols in the output)

Collection element QC_boxplot_peptide of collection plots:  different than expected, difference (using diff):
( /tmp/tmpj0sk7c5nQC_boxplot_peptide.pdf v. /tmp/tmpf91yf51dQC_boxplot_peptide.pdf )
--- local_file
+++ history_data
@@ -2,8 +2,8 @@
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-/CreationDate (D:20250109160515)
-/ModDate (D:20250109160515)
+/CreationDate (D:20250109153657)
+/ModDate (D:20250109153657)
 /Title (R Graphics Output)
 /Producer (R 4.4.2)
 /Creator (R)
@@ -17,28 +17,21 @@
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 8 0 obj
 <<
-/Length 7685 /Filter /FlateDecode
+/Length 7677 /Filter /FlateDecode
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 << /Type /Pages /Kids [ 7 0 R ] /Count 1 /MediaBox [0 0 504 504] >>
@@ -83,16 +76,16 @@
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 trailer
 << /Size 11 /Info 1 0 R /Root 2 0 R >>
 startxref
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[bgruening]

Ah its a PDF. PDF is hard to compare unfortunately. Maybe just check the size?

[hechth]

crazy, if I try running it with biocontainers I get a different error - cool, yeah will do size diff then

[hechth]

The bio.tools entry so far is just a dummy but the website seems somehow lagging a lot. Will update the record as soon as that will be fixed.

[bgruening]

Great work @KristinaGomoryova! Well done. This looks very good to me!

Not sure about Martin's last question, but from me +1!

Thanks a lot!