diff --git a/tool_collections/fastx_toolkit/macros.xml b/tool_collections/fastx_toolkit/macros.xml
index efb4fb60ede..e01b1056ce0 100644
--- a/tool_collections/fastx_toolkit/macros.xml
+++ b/tool_collections/fastx_toolkit/macros.xml
@@ -47,8 +47,8 @@
author = "Assaf Gordon",
title = "FASTQ/A short-reads pre-processing tools",
year = "2010",
- note = "http://hannonlab.cshl.edu/fastx_toolkit/",
- url = "http://hannonlab.cshl.edu/fastx_toolkit/"}
+ note = "https://github.com/agordon/fastx_toolkit",
+ url = "https://github.com/agordon/fastx_toolkit"}
diff --git a/tool_collections/snpsift/snpSift_macros.xml b/tool_collections/snpsift/snpSift_macros.xml
index 8442a34caa2..80f080a0e8d 100644
--- a/tool_collections/snpsift/snpSift_macros.xml
+++ b/tool_collections/snpsift/snpSift_macros.xml
@@ -24,7 +24,7 @@ SnpSift dbnsfp 2>&1|head -n 1
For details about this tool, please go to:
-- http://snpeff.sourceforge.net/SnpEff_manual.html
+- https://pcingola.github.io/SnpEff/
diff --git a/tool_collections/snpsift/snpsift/snpSift_filter.xml b/tool_collections/snpsift/snpsift/snpSift_filter.xml
index 9d6df6b5db8..b00b8f9a84b 100644
--- a/tool_collections/snpsift/snpsift/snpSift_filter.xml
+++ b/tool_collections/snpsift/snpsift/snpSift_filter.xml
@@ -214,13 +214,10 @@ Filtering based on SnpEff annotations (``ANN`` or ``EFF`` fields):
For information regarding HGVS and Sequence Ontology terms versus classic names:
-- https://pcingola.github.io/SnpEff/se_commandline/ for the options: ``-classic``, ``-hgvs``, and ``-sequenceOntology``
-- https://pcingola.github.io/SnpEff/se_inputoutput/#effect-prediction-details for the table containing the classic name and sequence onology term for each effect
+- https://pcingola.github.io/SnpEff/snpeff/commandline/ for the options: ``-classic``, ``-hgvs``, and ``-sequenceOntology``
+- https://pcingola.github.io/SnpEff/snpeff/inputoutput/ for the table containing the classic name and sequence onology term for each effect
@EXTERNAL_DOCUMENTATION@
-- https://pcingola.github.io/SnpEff/ss_filter/
-
-The second link in particular has further details and more examples about the tool's expression syntax.
]]>
diff --git a/tools/breseq/breseq.xml b/tools/breseq/breseq.xml
index 4a6a3fe60bb..797050597c0 100644
--- a/tools/breseq/breseq.xml
+++ b/tools/breseq/breseq.xml
@@ -296,9 +296,8 @@ breseq's primary advantages over other software programs are that it can:
- Produce annotated output describing biologically relevant mutational events.
breseq was initially developed to analyze data from the Lenski long-term
-evolution experiment with `E. coli`_. References: barrick2009a_ barrick2009b_.
+evolution experiment with E. coli. References: barrick2009a_ barrick2009b_.
-.. _`E. coli`: http://myxo.css.msu.edu/ecoli/
.. _barrick2009a: http://barricklab.org/twiki/pub/Lab/ToolsBacterialGenomeResequencing/documentation/references.html#barrick2009a
.. _barrick2009b: http://barricklab.org/twiki/pub/Lab/ToolsBacterialGenomeResequencing/documentation/references.html#barrick2009b
diff --git a/tools/delly/cnv.xml b/tools/delly/cnv.xml
index c294fecf308..81f8a09a1c8 100644
--- a/tools/delly/cnv.xml
+++ b/tools/delly/cnv.xml
@@ -190,7 +190,7 @@ $gc.nowindowselection
**Input**
-Delly *cnv* requires are a sample (BAM), a genome (FASTA) and a mappability map (FASTA), which is available `here `_. Intervals (BED), scanning regions (BED) and a delly SV file for breakpoint refinement (BCF) can be provided optionally.
+Delly *cnv* requires are a sample (BAM), a genome (FASTA) and a mappability map (FASTA), which is available `here `_. Intervals (BED), scanning regions (BED) and a delly SV file for breakpoint refinement (BCF) can be provided optionally.
**Output**
diff --git a/tools/disco/disco.xml b/tools/disco/disco.xml
index d6c62c36a0d..0f7d1277300 100644
--- a/tools/disco/disco.xml
+++ b/tools/disco/disco.xml
@@ -430,8 +430,8 @@ minEdgeLengthToBe1MinFlow = $third_assembly_iter_param.minEdgeLengthToBe1MinFlow
diff --git a/tools/dnaweaver/dnaweaver.xml b/tools/dnaweaver/dnaweaver.xml
index a57e639a7fa..869176c65fd 100644
--- a/tools/dnaweaver/dnaweaver.xml
+++ b/tools/dnaweaver/dnaweaver.xml
@@ -86,7 +86,7 @@ Method
Here is a schema of the supply network used:
-.. image:: https://raw.githubusercontent.com/brsynth/synbiocad-galaxy-wrappers/master/DNAWeaver/img/image4.png
+.. image:: https://github.com/brsynth/galaxytools/blob/main/tools/dnaweaver/img/image4.png?raw=true
:width: 30 %
:align: center
diff --git a/tools/genehunter_modscore/genehunter_modscore.xml b/tools/genehunter_modscore/genehunter_modscore.xml
index 6dc3011aa4c..ebd255655ce 100644
--- a/tools/genehunter_modscore/genehunter_modscore.xml
+++ b/tools/genehunter_modscore/genehunter_modscore.xml
@@ -463,7 +463,7 @@ Due to the stochastic nature of the analysis, a random seed can be set by the us
Many more configurable options are outlined in the the official manual_.
-.. _manual: https://www.helmholtz-muenchen.de/fileadmin/GENEPI/downloads/ghm-3.0.pdf
+.. _manual: https://web.archive.org/web/20131010145407/https://www.helmholtz-muenchen.de/fileadmin/GENEPI/downloads/ghm-3.0.pdf
]]>
diff --git a/tools/gprofiler/macros.xml b/tools/gprofiler/macros.xml
index 6ba8d4dfaec..90cd85aac7a 100644
--- a/tools/gprofiler/macros.xml
+++ b/tools/gprofiler/macros.xml
@@ -19,10 +19,9 @@
`_ the subnetwork of interest, linking the biosensor to the compound to be detected, and produce an interactive web page showing the transducing reactions.
+**rp2biosensor** is an open-source Python software that extracts from the retrosynthetic network generated by `RetroPath2.0 `_ the subnetwork of interest, linking the biosensor to the compound to be detected, and produce an interactive web page showing the transducing reactions.
-Briefly, rp2biosensor parses the retrosynthesis network outputted by RetroPath2.0, completes the predicted reactions by putting back co-substrates and co-products omitted during the retrosynthesis using the `rxn_rebuild `_ Python package, enumerates the shortest path linking the compound of interest, i.e. the biosensor, to the compound to be detected, e.g. lactate, and finally outputs the resulting subnetwork as an interactive web page to let the user browse the results.
+Briefly, rp2biosensor parses the retrosynthesis network outputted by RetroPath2.0, completes the predicted reactions by putting back co-substrates and co-products omitted during the retrosynthesis using the `rxn_rebuild `_ Python package, enumerates the shortest path linking the compound of interest, i.e. the biosensor, to the compound to be detected, e.g. lactate, and finally outputs the resulting subnetwork as an interactive web page to let the user browse the results.
Input
-----
diff --git a/tools/rptools/rpreport.xml b/tools/rptools/rpreport.xml
index ba7c7907a42..74b7c5b706d 100644
--- a/tools/rptools/rpreport.xml
+++ b/tools/rptools/rpreport.xml
@@ -54,7 +54,7 @@ rpReport
Generates HTML pages to explore the main characteristics (thermodynamics,
fluxes, number of metabolic steps, reaction rule score) of pathways predicted
-with `RetroPath suite `_.
+with `RetroPath suite `_.
Input
diff --git a/tools/rptools/rpviz.xml b/tools/rptools/rpviz.xml
index 5baca6fa0b6..c6104532ed6 100644
--- a/tools/rptools/rpviz.xml
+++ b/tools/rptools/rpviz.xml
@@ -82,7 +82,7 @@
RPVIZ
================
-Visualize pathways from the `RetroPath Suite `_.
+Visualize pathways from the `RetroPath Suite `_.
Input
-----
diff --git a/tools/slamdunk/slamdunk.xml b/tools/slamdunk/slamdunk.xml
index dad6cfd0cac..4b73d9a0934 100644
--- a/tools/slamdunk/slamdunk.xml
+++ b/tools/slamdunk/slamdunk.xml
@@ -175,7 +175,7 @@ SLAM-seq
SLAM-seq is a novel sequencing protocol that directly uncovers 4-thiouridine incorporation events in RNA by high-throughput sequencing. When combined with metabolic labeling protocols, SLAM-seq allows to study the intracellular RNA dynamics, from transcription, RNA processing to RNA stability.
-Original publication: `Herzog et al., Nature Methods, 2017; doi:10.1038/nmeth.4435 `_
+Original publication: `Herzog et al., Nature Methods, 2017; doi:10.1038/nmeth.4435 `_
Slamdunk
========
@@ -220,7 +220,7 @@ Parameter Description
T>C conversions
---------------
-Depending on the use case, more stringent or more lenient measures of T>C conversion and T>C reads are required such as 2 T>C by `Muhar et al., Science, 2018; http://doi.org/10.1126/science.aao2793 `_
+Depending on the use case, more stringent or more lenient measures of T>C conversion and T>C reads are required such as 2 T>C by `Muhar et al., Science, 2018; doi:10.1126/science.aao2793 `_
This can be controlled by the following parameter:
diff --git a/tools/structure/structure.xml b/tools/structure/structure.xml
index 5ea5aabf22a..a7a6f50bd43 100644
--- a/tools/structure/structure.xml
+++ b/tools/structure/structure.xml
@@ -533,7 +533,7 @@ You will find other sample data sets: here_
.. _Clumpp: https://rosenberglab.stanford.edu/clumpp.html
.. _Distruct: https://rosenberglab.stanford.edu/distruct.html
-.. _Structure-harvester: http://taylor0.biology.ucla.edu/structureHarvester/
+.. _Structure-harvester: http://alumni.soe.ucsc.edu/~dearl/software/structureHarvester/
]]>
diff --git a/tools/structureharvester/structureharvester.xml b/tools/structureharvester/structureharvester.xml
index 88428d5f7b7..85cff2238a1 100644
--- a/tools/structureharvester/structureharvester.xml
+++ b/tools/structureharvester/structureharvester.xml
@@ -89,7 +89,7 @@
Structure_Harvester_ is a program for parsing the output of Pritchard's STRUCTURE_ and for performing the Evanno method.
-.. _Structure_Harvester: http://taylor0.biology.ucla.edu/structureHarvester/
+.. _Structure_Harvester: http://alumni.soe.ucsc.edu/~dearl/software/structureHarvester/
.. _STRUCTURE: http://web.stanford.edu/group/pritchardlab/structure.html
]]>
diff --git a/tools/transit/transit_gumbel.xml b/tools/transit/transit_gumbel.xml
index d062a36af20..0b0e9bb67c3 100644
--- a/tools/transit/transit_gumbel.xml
+++ b/tools/transit/transit_gumbel.xml
@@ -123,8 +123,8 @@ Note: Technically, Bayesian models are used to calculate posterior probabilities
See `TRANSIT documentation`
-- TRANSIT: https://transit.readthedocs.io/en/latest/index.html
-- `TRANSIT Gumbel`: https://transit.readthedocs.io/en/latest/transit_methods.html#gumbel
+- TRANSIT: https://transit.readthedocs.io/en/v@TOOL_VERSION@/index.html
+- `TRANSIT Gumbel`: https://transit.readthedocs.io/en/v@TOOL_VERSION@/transit_methods.html#gumbel
]]>
diff --git a/tools/transit/transit_hmm.xml b/tools/transit/transit_hmm.xml
index 6c81f0ec982..fa0d5e8472e 100644
--- a/tools/transit/transit_hmm.xml
+++ b/tools/transit/transit_hmm.xml
@@ -120,6 +120,19 @@ State Call State Classification (ES = Essen
============================================= ========================================================================================================================
Note: Libraries that are too sparse (e.g. < 30%) or which contain very low read-counts may be problematic for the HMM method, causing it to label too many Growth-Defect genes
+
+
+-------------------
+
+**More Information**
+
+-------------------
+
+See `TRANSIT documentation`
+
+- TRANSIT: https://transit.readthedocs.io/en/v@TOOL_VERSION@/index.html
+- `TRANSIT Gumbel`: https://transit.readthedocs.io/en/v@TOOL_VERSION@/transit_methods.html#hmm
+
]]>
diff --git a/tools/transit/transit_resampling.xml b/tools/transit/transit_resampling.xml
index b3f6e6ce14f..dbffc22e264 100644
--- a/tools/transit/transit_resampling.xml
+++ b/tools/transit/transit_resampling.xml
@@ -144,8 +144,8 @@ p-adj. Adjusted p-value controlling for
See `TRANSIT documentation`
-- TRANSIT: https://transit.readthedocs.io/en/latest/index.html
-- `TRANSIT Gumbel`: https://transit.readthedocs.io/en/latest/transit_methods.html#re-sampling
+- TRANSIT: https://transit.readthedocs.io/en/v@TOOL_VERSION@/index.html
+- `TRANSIT Gumbel`: https://transit.readthedocs.io/en/v@TOOL_VERSION@/transit_methods.html#re-sampling
]]>
diff --git a/tools/transit/transit_tn5gaps.xml b/tools/transit/transit_tn5gaps.xml
index edb94f3f0a1..b24531a62b8 100644
--- a/tools/transit/transit_tn5gaps.xml
+++ b/tools/transit/transit_tn5gaps.xml
@@ -113,8 +113,8 @@ Note: Technically, Bayesian models are used to calculate posterior probabilities
See `TRANSIT documentation`
-- TRANSIT: https://transit.readthedocs.io/en/latest/index.html
-- `TRANSIT Tn5Gaps`: https://transit.readthedocs.io/en/latest/transit_methods.html#tn5gaps
+- TRANSIT: https://transit.readthedocs.io/en/v@TOOL_VERSION@/index.html
+- `TRANSIT Tn5Gaps`: https://transit.readthedocs.io/en/v@TOOL_VERSION@/transit_methods.html#tn5gaps
]]>
diff --git a/tools/velvet/macros.xml b/tools/velvet/macros.xml
index aa642d01265..f2998df50cf 100644
--- a/tools/velvet/macros.xml
+++ b/tools/velvet/macros.xml
@@ -11,10 +11,10 @@
-
+
-
+
@@ -24,5 +24,17 @@
+
+**What it does**
+
+Velvet is a de novo genomic assembler specially designed for short-read sequencing technologies, such as Solexa or 454, developed by Daniel Zerbino and Ewan Birney at the
+European Bioinformatics Institute (EMBL-EBI), near Cambridge, in the United Kingdom.
+
+Velvet currently takes in short read sequences, removes errors, and then produces high-quality unique contigs. It then uses paired-end read and long read information, when available, to retrieve the repeated areas between contigs.
+
+Read the Velvet `documentation`__ for details on using the Velvet Assembler.
+
+.. __: https://github.com/dzerbino/velvet/blob/master/Manual.pdf
+
diff --git a/tools/velvet/velvetg.xml b/tools/velvet/velvetg.xml
index daeb3ccfae8..cac02a775d5 100644
--- a/tools/velvet/velvetg.xml
+++ b/tools/velvet/velvetg.xml
@@ -214,17 +214,7 @@